Defensive coordinator Wes Goodwin said Monday that Thomas, a 6-foot-5, 265-pound fifth-year lineman, will need surgery.
Thomas hurt himself during a scrimmage Saturday and tweeted afterward: "Small thing to a GIANT. The work does not stop! Ill be right back."
A Clemson spokesperson said in a text to The Associated Press that he didn't know if Thomas injured his right or left foot.
Thomas had 27 tackles, including 3½ sacks and two forced fumbles in 12 games last season, 10 of them starts. Thomas, who is from Florence, South Carolina, has started 19 games in his Clemson career, with 112 tackles and 12½ sacks.
Goodwin is hopeful that Thomas could return in time for No. 4 Clemson's game at 22nd-ranked Wake Forest, the defending ACC Atlantic champion, on Sept. 24.
"Unfortunate setback, but he's got the right mindset and he'll respond, [we'll] get him back early in the year," Goodwin said.