Thomas R. Kendrick, director of operations of the Kennedy Center, will resign his position in September to become executive director of the Orange County Performing Arts Center, an $85.5 million arts facility currently under construction in Southern California.

In his new post, he will be responsible for the operation and programming of the three-theater complex, which will include a 3,000-seat home for musical theater, opera, dance and symphony orchestras. The privately financed facility, described by Kendrick as "the last of the major arts centers to be built in the country," is scheduled to open by October 1986.

"This is a new challenge of major proportions for me," Kendrick, 51, said yesterday. "Orange County is an affluent and populous area and I think it has real potential for becoming a national arts center. The community energy and private support behind it are impressive. They're going first-class."

Kendrick joined the Kennedy Center in 1976 as an aide to chairman Roger L. Stevens, who said yesterday that Kendrick has been "a first-rate administrator and an invaluable right hand to me, but he's had a great offer and he'd be crazy not to take it."

Kendrick declined to disclose his new salary, saying that it was in the six-figure range and that it represented "a substantial advance" over his Kennedy Center wages and included "very generous benefits.

As one of his first staff appointments, Kendrick has hired another Kennedy Center employe, Judith O'Dea Morr, to be general manager in charge of technical theater and production details at the Southern California facility. In July, Morr, 43, will resign her current position, general manager of theaters, in which she has handled contractual negotiations and production logistics for incoming shows.

Stevens said that he is looking for a replacement for Morr, but that Kendrick's job at the Center will probably cease to exist as presently constituted. "Tom's duties will be realigned and divided up. I expect to bring on a new financial officer. But I don't think there will be anyone doing specifically what he was doing, which was a lot," he said.

At the Center, Kendrick has exercised wide-ranging authority over such matters as personnel, labor relations, budgets and education programs, and was one of the key players last fall in the successful lobbying effort to get Congress to restructure the Center's debt. He has had less influence on artistic policy, generally considered to be Stevens' preserve, although that will become a significant part of his new job in Costa Mesa.

Kendrick's resignation comes at a time when the Center has been undergoing radical changes, with the establishment of the American National Theater (ANT) under the direction of Peter Sellars. Both Stevens and Kendrick denied any connection between the two, however. "My leaving has nothing to do with Peter's coming here," Kendrick said. "I was always an advocate of ANT. If anything, I'm considered around here as too much of an advocate. But I saw it (ANT) as good from a programming point of view and good from an economic point of view in light of the state of theater today."

Kendrick's appointment will be announced this afternoon in Costa Mesa by officials of the Orange County Performing Arts Center, who first approached him last September and consider his experience at the Kennedy Center as critical to the success of their operation. "It's like a great gift from our nation's capital," said Timothy L. Strader, president of the Orange County Center's board.

Besides housing touring attractions, the Orange County Performing Arts Center will be the official home of the South Coast Repertory, one of Southern California's leading regional theaters.

Before joining the Kennedy Center staff, Kendrick was an assistant managing editor at The Washington Post, in charge of the Style section.