Djibril Cisse briefly looked to have won it for Harry Redknapp's side but McCarthy popped up with his second of the game minutes later to deny QPR and leave them deep in the mire.
McCarthy had opened the scoring in the first half with a fine volley but Ryan Nelsen equalised for the visitors with a header soon after.
Wigan boss Roberto Martinez had major defensive worries going into the game as his first-choice back-three were all unavailable through a combination of injury and suspensions.
That showed in a nervy opening as the Hoops, with Stephane Mbia and Samba Diakite prominent in midfield, looked the more purposeful of the sides without troubling Ali Al Habsi in the Latics goal.
But it was Wigan that took the lead in fine style inside 20 minutes when McCarthy volleyed low into Robert Green's net after Jamie Mackie had failed to effectively clear a corner from the left.
Redknapp's apparent decision to favour perspiration over inspiration in leaving so many of his flair players on the bench looked to have backfired.
But they were back on level terms just seven minutes later thanks to their wholehearted captain when Nelsen rose to head powerfully home at the near post from Adel Taarabt's corner.
Wigan came out a much-improved team after the interval as they completely dominated the early stages of the second half with QPR retreating into their shell.
David Jones forced Green into a smart save with a volley and then the former England goalkeeper was beaten by Jordi Gomez only for the ball to come back off the crossbar.
But when Adrian Lopez misplaced a pass in defence, Shaun Wright-Phillips picked out Cisse on the edge of the box who guided the ball left-footed into the corner to punish Wigan on the break.
There was no happy ending for the Premier League bottom club though and when Jean Beausejour measured his cross to find McCarthy, the Irishman slotted past Green to earn a point for his team.
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