The Wales international's MRI scan revealed he ruptured his cruciate ligament in Saturday's 1-0 win over Birmingham.
He will undergo knee surgery this week and be sidelined for six months so a pre-season return looks on the cards.
Boss Oscar Garcia told the club's official website: "I am very sorry for Crofty, he has been excellent this season and a key player. He wanted to play a big part in our season after missing so much of the last campaign through injury.
"Of course, he has already done that, with his performances and the key goals he has scored, and he will be a big loss - but we have a good squad with strength in depth to deal with this type of situation.
"On behalf of all at the club I would like to wish him a speedy recovery."