The loss of Merriman, whose hard hits earned him the nickname "Lights Out," is a big one for a team that has Super Bowl expectations.
Merriman's decision came two days after he barely resembled the player who had an NFL-high 39½ sacks in the past three seasons and played in three straight Pro Bowls.
Merriman, known for his spasmodic sack dance, didn't immediately return e-mails and telephone calls seeking comment. His agent, Tom Condon, declined to comment.
"Shawne informed me he did not feel right and thought it best to shut it down," Chargers general manager A.J. Smith said in a statement. "The road to winning the AFC West just got more difficult, but not impossible. Nothing is impossible. Shawne is a great player and an inspirational leader. He will be missed. We wish him a successful surgery and a speedy recovery."
Smith didn't return calls seeking further comment.
Merriman had only two tackles and no sacks in a shocking 26-24 loss to Carolina at home on Sunday. Even though Merriman appeared to be a non-factor, coach Norv Turner said he thought the linebacker looked "explosive and very physical."
Merriman wore a brace on the knee on Sunday. At one point, he had to go into the locker room to have it readjusted because it was slipping due to sweat.
The Chargers were outgained 388-316 on Sunday by a Panthers team playing without leading receiver Steve Smith.
The Chargers are also without inside linebacker Stephen Cooper, who was suspended by the NFL for the first four games this season for testing positive for a banned stimulant. Cooper led the Chargers with 179 tackles last season, when San Diego won the AFC West at 11-5 and reached the conference championship game before losing 21-12 at New England.
Late in training camp, Merriman said that the posterior cruciate and lateral collateral ligaments in his left knee were torn.
He spent several days getting opinions from four doctors from outside the organization, all of whom recommended he have surgery. But on Aug. 27, he announced that he was going to play, saying, "If you give a football player a decision to play, you know, I'm going to play."
But, he acknowledged, "I'll have the surgery at any point. Nobody knows. I kind of left it on the table when to have it. Not even doctors can tell me that."
Rehab is expected to be six to seven months.
Merriman has said he's had pain in the knee since late in the 2006 season. He also injured the knee during a game at Tennessee on Dec. 9. He sat out the following Sunday, but played in the last three regular-season games and the Chargers' three playoff games, including the loss to New England. He also played in the Pro Bowl.
Merriman had offseason arthroscopic surgery to repair torn cartilage in the knee.
Second-year pro Jyles Tucker is expected to take Merriman's spot. Tucker, who has played in only seven regular-season games, received a five-year contract extension two days before Merriman announced he was going to play rather than have surgery.
Merriman was suspended for four games in 2006 after testing positive for steroids. Both he and his lawyer blamed it on a tainted supplement. The Chargers went 4-0 in his absence.