Hosts claim the points in Greater Manchester
Second-half goals from Kieran Lee and Dapo Afolayan saw Bolton condemn Town to defeat.
In what was largely an evenly-matched game, Sone Aluko went closest to putting the Blues in front before the hosts struck twice in the last 16 minutes to claim the spoils.
Kieran McKenna named an unchanged side from last Saturday's victory over Gillingham, with Bersant Celina replacing Kayden Jackson on the bench in the only alteration from the trip to Kent.
Town created the first opening of the game on 15 minutes. The move began with a surging run from Janoi Donacien, who won possession back before beating a man and playing the ball inside to Lee Evans, who offloaded to Sam Morsy. Having switched the ball from right to left, the Blues worked the ball inside to Aluko, who saw his low shot from the edge of the area parried by Bolton shot-stopper James Trafford.
The hosts could've taken the lead four minutes later but Dion Charles headed Lee's cross wide of the mark.
Charles went closer with just over half an hour played but, after racing past the Blues' backline, his left-footed shot was turned around the post by a brilliant diving save from Christian Walton. The Trotters finished the first half on top, albeit with creating any chance of note, Gethin Jones blazing a half-volley high and wide following a corner late in the opening period.
Aluko was inches away from giving Town the lead shortly after the restart, his curled effort from just outside of the area falling wide of the top left corner. Aluko had another good opening three minutes later following good work from Matt Penney but the midfield this time seeing a low right-footed effort blocked behind by Ricardo Almeida Santos.
Bolton took the lead on 74 minutes. After working the ball to the edge of the area, Aaron Morley saw a low shot parried by Walton but Lee was in position to blast the rebound into the roof of the net from close range.
Luke Woolfenden nearly found an instant equaliser but, after a corner routine by Aluko and Evans, the centre-back's header was straight at a well-positioned Trafford.
Instead, the hosts put the game to bed by doubling their advantage 10 minutes from time, with Afolayan capitalising on a defensive mix-up before slotting underneath Walton.
Town saw the majority of the ball in the closing stages, Bersant Celina and George Edmundson going close to what would have been a consolation goal, but the hosts held on to claim the three points.
Bolton: Trafford, Jones (Aimson 90'), John, Williams, Almeida Santos (C), Johnston, Charles (Afolayan 70'), Bakayoko (Delfouneso 90'), Fossey, Morley, Lee.
Subs: Dixon, Thomason, Baptiste, Gordon.
Booked: Williams, Almeida Santos.
Town: Walton, Donacien, Woolfenden, Edmundson, Burns, Evans, Morsy (C), Penney (Vincent-Young 70'), Aluko (Chaplin 82'), Norwood (Celina 70'), Bonne.
Subs: Hladky, Burgess, Carroll, Pigott.
Booked: Walton, Norwood, Burns.