Carroll sustained the injury during West Ham's 0-0 draw at Southampton on Wednesday, but remained on the field until the end of the game.
The striker was seen leaving St Mary's Stadium on crutches, and manager Sam Allardyce was initially quoted as saying he would be out for at least four weeks.
A club statement read: "Andy Carroll will have surgery on his injured knee on Tuesday following assessment by a specialist on Friday afternoon.
"The recovery phase is expected to keep Carroll out for the remainder of the 2014-15 season."
The news comes as a huge blow to both club and player, with Carroll having netted five goals in 14 Premier League outings in 2014-15.
It represents yet another serious injury setback for Carroll, who did not feature until November due to an ankle problem and missed much of last term with a heel issue.
Carroll's knee injury is a recurrence of an earlier issue, and means the goalscoring burden at West Ham will now fall largely on the likes of Diafra Sakho, Enner Valencia and Carlton Cole.
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