After failing to agree on a contract extension with the Thunder, Harden was traded to the Houston Rockets, along with Daequan Cook, Cole Aldrich, and Lazar Hayward, for Kevin Martin and Jeremy Lamb, two first round picks and a second round pick.Rockets general manager Daryl Morey called Harden a "foundational" player for the team's goal of returning to title contention.Harden was expected to be Houston's featured player after starting only seven games in three years in a supporting role behind Durant and Westbrook. On October 31, he signed a contract extension with the Houston Rockets for five years worth $80 million.In the Rockets 2012–13 season opener, he had 37 points, 12 assists, six rebounds, and four steals. His 37 points tied for the second most for an NBA player in his debut with a new team, and he was also the first with at least 37 points and 12 assists in his debut. Harden was the first Houston player to record 37/12 since Hakeem Olajuwon in 1994–95. On November 2, 2012, he scored 45 points in a win against the Atlanta Hawks; he also tallied 7 rebounds and 2 assists. Following the first week of the season, Harden was named the Western Conference Player of the Week.
Harden was named the Western Conference Player of the Week for the second time for games played between December 30th and January 6th after averaging 29.3 points, 5.5 assists, and leading the Rockets to a perfect 4-0 week, including two double-digit comebacks on the road.
On January 10, 2013, during a loss to the New Orleans Hornets, Harden scored 25 points for the 14th consecutive game, breaking the Rockets' franchise record previously held by Hall of Famer Moses Malone.
Harden was named to his first All-Star game as a reserve for the Western Conference for the 2012–13 season. He was one of seven first-time selections, along with Kyrie Irving, Paul George, Jrue Holiday, Tyson Chandler, Joakim Noah, and Brook Lopez, although Harden was the only first-time All-Star for the Western Conference. Harden scored 15 points in the game.