The 24-year-old suffered the setback against his former club Manchester United in the Carling Cup at Old Trafford.
Jones tried to train ahead of last weekend's clash with Sunderland but was not fit enough to play at the Stadium Of Light.
He underwent a scan and his worst fears have been realised, with the ex-England Under-21 player out of action until the start of December.
McCarthy confirmed: "Jones has had a clean-up operation in his knee and will be out for two months.
"He felt it against Manchester United and thought it was just a bit of swelling. He tried to train in the build-up to the Sunderland game but it wasn't right.
"He had a scan and has had the surgery on the knee."
Jones joined Wolves last summer from Derby in a £1million deal and made 37 appearances in helping them gain promotion back to the Premier League.
But this season he has made just one league appearance as a substitute against Wigan in addition to appearing against Swindon and the Red Devils in the Carling Cup.
McCarthy has no other fresh injury worries ahead of the home league clash with bottom club Portsmouth on Saturday.