Harden suffered the injury while driving for a layup in the fourth quarter of a game against the Los Angeles Lakers on Sunday.
The Rockets said he will be re-evaluated in two weeks.
Harden is averaging 32.3 points per game along with 9.1 assists and is a leading candidate for the league’s MVP Award.
Houston (26-9) have lost five of their last six games to fall to second in the Western Conference.
ESPN reported on Monday that Harden's injury is a Grade 2 hamstring strain. The network pointed out Harden's history of durability, too. The 28-year-old has only missed two games since the start of the 2014-15 NBA season.
Harden's importance to the Rockets was shown up on Sunday against the Lakers. The guard had 40 points and 11 assists as the Rockets outlasted a Lakers squad that is itself without starting point guard Lonzo Ball.
Sports Illustrated, for one, thought the Rockets capable of surviving without Harden for now.
"At first blush, Houston appears to be capable of surviving without Harden. In 196 minutes with Chris Paul on the court and Harden off this season, the Rockets have a net rating of 21.5, which is actually much better than Houston’s net efficiency when Paul and Harden are playing together," Rohan Nadkarni wrote on Monday. Paul, who signed as a free agent from the L.A. Clippers in the summer, missed a significant portion of the autumn for the Rockets.
"When Harden returns and gets back up to speed, the Rockets will certainly soon resume destroying opponents under a barrage of 3-pointers and rim runs, deflections and snuffed shots at the rim that lead to runouts, and fourth quarters for Harden and Paul with ice on their knees," David Aldridge wrote for NBA.com on Monday.
In the meantime, the Rockets will have to lean on Paul for creativity and scoring. Houston faces the lowly Orlando Magic on January 4, a game that shouldn't give them much trouble with or without Harden.
A night later, on January 5, the Rockets take on the Golden State Warriors. The Harden-Paul combination was made for games like these against the defending NBA champions. But Houston's season has rarely gone to plan so far.