The visitors dominated the first hour of the game, and it was only when they eased off the gas that Ipswich came into it.
Former Ipswich loanee Alan Mahon fired wide from 20 yards after two minutes before centre-half Ian Breckin hooked wide when Ipswich failed to clear a corner.
Only a fine goal-line clearance from Matt Richards denied Jason Roberts a goal on seven minutes after he collected a Jimmy Bullard pass and rounded goalkeeper Kelvin Davis.
Still the danger wasn't over, but Nathan Ellington blazed wide from the rebound, before his flick put Roberts clear, but Davis blocked his shot.
A goal looked certain for Wigan and it arrived on 18 minutes when Driss Diallo missed a headed clearance and Roberts raced clear to calmly shoot beyond Davis.
Seconds later Davis dived to tip away a Gary Teale drive, before Town's first clear chance saw Shefki Kuqi head a Chris Bart-Williams cross over.
Wigan doubled their lead on 33 minutes, Teale crossing for an unmarked Ellington to side-foot in after a superb long ball from Nicky Eaden.
Town boss Joe Royle made two half-time substitutions and one, Darren Bent, set up skipper Jim Magilton within a minute of the re-start but he blazed over.
Wigan sealed the points with a fantastic third goal on 53 minutes, Teale smashing a shot in off the bar from 20 yards out.
Kuqi scored a consolation goal for Town on the hour-mark, converting a Magilton pass, but the visitors comfortably held on to record a league double over Ipswich, despite the late sending off of left-back Leighton Baines for two bookable offences in the space of eight minutes.