After a goalless first half of few real chances, substitute Nathan Arnold opened the scoring just after the hour.
Arnold was also influential in Grimsby’s second goal, as his shot was blocked before Lenell John-Lewis headed in the rebound.
And the same combination led to a third goal with a quarter of an hour to go, as John-Lewis tapped in at the far post after Arnold cut in and hit the ball across goal.
Two changes were made to the Town side after the win at Torquay last week, with Craig Clay replacing Danny Parslow after he was recalled by parent club York City and Ross Hannah coming in for the injured Scott Brown.
That meant a switch to a 4-4-2 formation, with goalkeeper James McKeown behind a defence of Carl Magnay, Aristote Nsiala, Shaun Pearson and Aswad Thomas.
The midfielders were Jack Mackreth, Craig Disley, Clay and Scott Neilson, while Hannah lined up alongside John-Lewis in attack.
Seven substitutes are allowed in FA Cup games, so Paul Bignot, Ellis Humble, Jon-Paul Pittman, Paul Walker, Caine Winfarrah, Paddy McLaughlin and Arnold all took their places on the Grimsby bench.
Guiseley made the journey from West Yorkshire looking to cause an upset but also prove they are able to compete with Conference Premier-standard clubs after missing out on promotion to non-league’s top tier through the play-offs in each of the last four seasons.
Boshell joined his younger brother Nicky in the starting XI. The Lions included a familiar face in the shape of former Town midfielder Danny Boshell, who is also assistant manager to Mark Bower.
Another to watch out for would be ex-Scunthorpe United striker Adam Boyes, who has also faced the Mariners in the colours of York City and Barrow.
Hannah hit the wall from the free kick and Thomas struck the rebound wide. Boyes had the first shot of the game but saw his 18-yard effort blocked, before John-Lewis had a shot deflected wide, although the referee brought play back for a foul on Hannah 20 yards out.
Town were now starting to take the initiative and they had a good chance to open the scoring on six minutes when Mackreth’s cross found John-Lewis but the striker could only head it over the bar.
The first corner of the game went to the Mariners two minutes later but did not cause visiting keeper Steve Drench any problems.
From the free kick, Neilson looked to place the ball into the far corner of the net but Drench dived to push it away for a corner, which was headed over the top by Nsiala. Hannah was caught late by midfielder Andy Holdsworth, who was shown the first yellow card of the afternoon for the challenge on 18 minutes.
Nicky Boshell’s shot hit the Town wall and the ball was brought clear by Mackreth. Guiseley were yet to threaten at the other end but they were handed a free kick when Gavin Rothery was brought down.
A move from the hosts soon afterwards following a throw-in eventually led to Magnay shooting from 20 yards but a deflection took the sting out of it and the ball went through to Drench.
The game stopped briefly after Wayne Brooksby was caught on the head by Disley as the pair contested the ball but the Guiseley midfielder was passed fit to continue after receiving treatment.
Nicky Boshell’s free kick eventually fell for Holdsworth but his shot went wide for a goal kick. Brooksby was then fouled by Thomas on the visitors’ right, five years outside the penalty area.
After the half-hour passed without a goal, Town’s next chance saw Neilson find John-Lewis with a cross from the left but he could not direct his header towards goal.
A foul on Hannah then gave the Mariners a free kick on the right on 35 minutes. Neilson played the ball back for Hannah, who drilled a low effort wide.
Another free kick came when Clay was brought down inside the Guiseley half but this time, Neilson’s ball into the box was cleared.
A cross from Neilson on the left was headed down by John-Lewis five minutes before the break but it took a touch off a defender and went out for a corner, from which Town could not cause any problems.
Clay then looked to have found his way through the Guiseley defence four minutes later but he was penalised for a handball.
A cross from Brooksby was comfortably taken by McKeown in a rare attack from the visitors, before a centre by Mackreth was blocked for a corner, which eventually led to Hannah heading over the bar.
Two added minutes were played at the end of the half and Hannah was given a chance from a free kick 25 yards out, from which he failed to hit the target.
And with no further opportunities for either side, the game remained goalless at the interval.
Town had been the better side but would have been disappointed not to have caused more danger for Drench and his back four.
Arnold replaced Neilson for Town before the restart, with Oli Johnson coming on in place of Nicky Boshell for the away side.
The hosts looked to make a quick start when John-Lewis played the ball for strike-partner Hannah but his shot from an acute angle went wide of the far post.
This time, Clay got the ball away. Brooksby won a corner for Guiseley two minutes in and the Mariners struggled to clear their lines until Mackreth had to head behind for another flag-kick on the opposite side.
A foul on Mackreth gave Grimsby a free kick on the right on 55 minutes and after the ball was played to Hannah, he turned and shot from the edge of the box but Drench got down to make a relatively comfortable stop.
At the other end, a free kick from Danny Lowe led to the ball being sent over the bar as McKeown’s lack of serious action so far continued.
Guiseley’s second substitution saw former Bradford City striker Danny Forrest come on for Boyes, who had not really made an impact on the game.
Town finally broke the deadlock just after the hour when a cross from Mackreth on the right sailed over keeper Drench and went through to the far post, where ARNOLD nodded it into the empty net.
Guiseley’s response came through a shot by Brooksby from 20 yards but it was straight at McKeown, who caught the ball.
A cross to the far post from Magnay was headed out for a Town corner by Jake Lawlor but Arnold’s delivery was headed clear.
Disley won another corner on the right on 66 minutes and this time, the skipper headed over the bar after the ball was missed by keeper Drench.
Arnold set off on a run through the Guiseley defence and after his shot was blocked by Drench, JOHN-LEWIS was there to head the rebound into the net. The Mariners were now well on top and they doubled their advantage a minute later.
Hannah looked to get his name on the scoresheet with a run and shot from 20 yards but he could not find the net.
A short spell of Guiseley pressure followed as the visitors looked to get themselves back in the game but to no avail.
Mackreth had an opportunity to kill the game off on 70 minutes but his shot from a narrowing angle on the right was parried away for a corner by Drench.
John-Lewis won a corner as the hosts continued to dominate but Pearson’s glancing header from Arnold’s corner went wide of the mark.
Again, Arnold was the architect, cutting in from the left and firing the ball across goal for the striker to tap in at the far post. The game was made safe 15 minutes from the end when JOHN-LEWIS grabbed his second of the game.
John-Lewis was denied the chance to complete a hat-trick as he was replaced by Pittman on 78 minutes, while Jack Stockdill came on in place of Danny Boshell for the visitors at the same time.
The final Grimsby change introduced Walker in place of Hannah with nine minutes left on the clock.
Four added minutes were played at the end of the game and a late Guiseley penalty appeal was turned down after substitute Johnson went down in the box in front of the 142 travelling supporters.
Town then looked to run the clock down, with Thomas winning a free kick near the corner flag but Arnold’s ball was cleared.
That proved to be the last action as the Mariners secured their place in the next round and they will find out their opponents in Monday’s draw.
Town then return to league action when Dartford visit Blundell Park on Saturday.