The 19-year-old was left writhing in agony following Fabrice Muamba's challenge midway through the first half and received lengthy treatment on the pitch before leaving on a stretcher.
McCarthy, who has played in all Wigan's Premier League games this season, was then taken to hospital, and player and manager must now wait for the results of an X-ray that will determine how long he will spend on the sidelines.
Martinez said: "He's gone to the hospital and we'll get the results over the next 24 hours but it doesn't look too good.
"It's a real shame because he's a very young man but he's very mature on the pitch and he's been performing in a very special manner."
The Spaniard, though, did not attach any blame to Muamba for the challenge, which was from behind but came after Latics captain Antolin Alcaraz put his team-mate in trouble with a poor pass.
"It's a difficult ball for a midfielder - it's a straight ball," continued Martinez. "When you look at the replay, he clearly gets his ankle first.
"It's disappointing. The intent is to play the ball. It's from behind.
"It's one of those actions - you're sending your team-mate into the lion's den. But he's young and he's very, very fit and we hope it's not as bad as it looks."
Bolton boss Owen Coyle saw the situation in much the same way and is keeping his fingers crossed McCarthy is not seriously injured after watching him come through the ranks at Hamilton, who he left to join Wigan last summer.
Coyle said: "My thoughts are to make sure he's okay because I've known him as a young kid progressing all the way through in Scotland to where he is now, and there's no doubt he's destined for a glittering career.
"Hopefully he's back very soon. Certainly from my position it looked an innocuous challenge. They both went to shut the ball."
Bolton began the game much the better but failed to test Chris Kirkland, and the break in play for McCarthy's injury actually seemed to help Wigan, who slowly came into the game.
They ended the first half with Charles N'Zogbia and Hugo Rodallega both troubling Jussi Jaaskelainen, and in the 59th minute the Latics took the lead when N'Zogbia and Franco Di Santo set up Rodallega for a clinical finish.
The advantage was a deserved one but it took only seven minutes for Bolton to level as a ball into the box caused problems for the home defence and Johan Elmander tucked away the equaliser.
Coyle was angry Rodallega's goal was allowed to stand but praised his side for the way they fought back.
"We went behind to a goal that was clearly two yards offside," he said. "I felt that in real time, I've seen it again and when Di Santo picks the ball up he's two yards offside. He's not even close.
"It would have been easy at that stage to feel sorry for ourselves having put so much into the game in the early part but this group of players, the spirit they have and the belief that they have, picked themselves up and really pushed on.
"We got a deserved equaliser and in the last part of the game both teams went all out to try to win the game."
Martinez was disappointed his side could not hold onto their advantage but took pride in a fourth Premier League game without defeat.
He added: "The start of the derby was a little bit up in the air. There was not too much quality, a lot of passion in the first 20 minutes.
"The last 25 minutes in the first half we finished really strong and you could see the goal was coming.
"I was extremely proud of the second-half performance. You're starting to see really good combinations. The team is starting to gel together and that's really pleasing."