Harden had 29 points, 14 assists and 10 rebounds in the Nets' 132-114 win to hand the Rockets their 13th consecutive loss. It was his eighth triple-double this season.
Brooklyn set a franchise record with its seventh straight road victory. The Nets have now won 10 of their last 11 games.
Harden received a mixed reception from the small crowd of 3,615 fans at Toyota Center in Houston. Many of the fans jeered the nine-time All-Star selection when he was introduced before the game and more boos echoed through the arena the first few times he touched the ball.
During a timeout in the first quarter, the Rockets honored Harden by playing a short video on the jumbotron. The video showcased some of Harden's best moments throughout his eight seasons in Houston.
There were more cheers than boos as the video played. Once the video ended, Harden stepped out of the Nets' huddle and raised his arms before placing his hands in a praying position to acknowledge the fans.
Harden, the 2018 NBA Most Valuable Player, spent eight-plus seasons with the Rockets before demanding a trade in January. Shortly after, the team traded him to the Nets in a blockbuster four-team deal.
Entering Wednesday's game, Harden was averaging 25.3 points, 11.3 assists and 8.7 rebounds across 22 contests with the Nets this year.