The 7-foot-6 Yao chose a surgery that will involve a bone graft to promote bone regeneration, the team said. He's also hoping to reduce the arch in the foot by realigning and restructuring the bones.
The team would not say definitively if Yao would miss all of next season.
"While no timetable has been set for his return to action, Yao is expected to be available for the team's training camp in 2010," the Rockets said. That camp is in October.
The decision for surgery was expected. The Rockets applied for a disabled player exception from the NBA a few weeks ago, betting that their center will miss next season as he recovers. The NBA agreed that Yao's return is unlikely and approved the request, freeing up about $5.7 million that the Rockets used to sign free agent Trevor Ariza from the Lakers.
Houston has also scrambled to find a center since free agency began and this week acquired 6-foot-11 David Andersen in a trade with Atlanta.
Yao has been consulting with doctors since late June, when the Rockets said he would be out indefinitely. He suffered a hairline fracture in the foot in a playoff game on May 3 and the team initially said Yao would miss only 8-12 weeks. When doctors re-examined the injury about seven weeks later, they discovered that the injury had not healed and amended the prognosis.
Dr. Tom Clanton, the Rockets' team doctor, will perform the surgery. He said Cleveland Cavaliers center Zydrunas Ilgauskas had a similar procedure in 2001 that allowed him to return to action.
"This combination of procedures should not only allow healing of his navicular stress fracture, but also improve the mechanics of his foot to reduce the stress on that bone and give him the best long-term prognosis," Clanton said in a statement.
John Huizinga, Yao's agent, did not immediately return a phone message.
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