Terms were not disclosed, but Crane told MLB.com that Hinch "will be here a while."
Hinch, 41, was hired following the 2014 season to replace Bo Porter, who was fired after two years in Houston, during which the team went a combined 121-203.
Led by Dallas Keuchel, the 2015 American League Cy Young Award winner, the Astros went 86-76 in Hinch's first year at the helm and sat atop the AL West for much of the season before earning a spot in the wild-card game, where they beat the New York Yankees. The club then lost to the eventual World Series champion Kansas City Royals in the AL Division Series.
"We could see last year he really had a lot of continuity in the locker room, and [he] continues to get these guys to jell," Crane told MLB.com. "He communicates well with the front office, and he and [Astros general manager] Jeff [Luhnow] work well together. We thought we had a good combination there. And we wanted to reward him for last year and give him some security and move the contract down the line a little bit."
Before his arrival in Houston, Hinch, a former catcher, managed the Arizona Diamondbacks for parts of the 2009 and 2010 seasons, going 89-123. He then served as vice president of professional scouting for the San Diego Padres before resigning in August 2014.