President Reagan yesterday nominated the handpicked successor of William D. Ruckelshaus, Lee M. Thomas, to be promoted to head the Environmental Protection Agency.

Ruckelshaus said he was not resigning as administrator over policy differences with the White House. But he acknowledged yesterday in an interview that he would have found it "difficult" to defend EPA budget cuts before Congress. He also said it was "not pleasant" at times to serve an administration that ousted his wife, Jill, from the U.S. Commission on Civil Rights.

He also said he plans to take a prominent role, possibly in Washington, in trying to depoliticize the conflict between environmentalists, the administration and industry, which he said has undermined environmental protection and prevented enactment of important statutes.

Ruckelshaus, in a wide-ranging interview, said he blames the polarization not only on environmentalists and some business leaders, but also on the administration.

"In the first two years [of the administration], there was a feeling among some in industry and the administration that they had the upper hand, and I frankly think that hand was overplayed," Ruckelshaus said. "I think they went too far in suggesting changes ought to be made and the country reacted.

"Then the pendulum shifted, and the environmentalists felt they had the upper hand. I frankly think they overplayed their hand, too . . . . Their constant barrage of criticism of this agency runs the risk of weakening the very institution on which the strength and well-being of their cause rests."

Ruckelshaus said he has not decided what to do after leaving the agency on Jan. 5, saying only that he knew it was time to resign. He said he believed that he had accomplished what he set out to do and that to go further -- to win reauthorization of many environmental laws -- would have required a longer tenure than he wanted.

"It's very important in these government jobs to sense when it's time to move on. There is a point when you start diminishing the returns you can get. I've relied on my stomach to tell me when that's true," he said.

The departing administrator, who took over the agency in 1983 amid a national scandal over EPA mismanagement and improper industry influence, said he felt his major accomplishment was that he had helped restore the agency's morale and credibility, an assessment echoed yesterday by many members of Congress, agency employes and environmentalists.

But Ruckelshaus listed among his disappointments his failure to put in place a system to control acid rain (his initiative was blocked by the White House and Office of Management and Budget Director David A. Stockman) and to win reauthorization of the Clean Air Act, the Clean Water Act, the Safe Drinking Water Act and the federal laws regulating pesticides and toxic substances.

Those statutes have expired, and Ruckelshaus had said he hoped to see them reauthorized before his departure. He succeeded only in winning congressional reauthorization of the Resource Conservation and Recovery Act, which vastly expanded control over generators of hazardous wastes.

A close associate of Ruckelshaus who talked to him after his resignation said his frustration played a major role in his decision to leave, although it was not tied directly to the fiscal 1986 budget. Sources said the EPA budget is not likely to be marked for 30 percent cuts, as charged by environmentalists.

"The administration hadn't shown that they cared much about the environment or were going to do anything about it . . . ," the associate said. "If there was one thing that rankled, it was the acid-rain decision. He [Ruckelshaus] worked out a middle ground. He fought it through the process and lost to Stockman at the last moment. . . . He's known all along that it wasn't going to get better."

An administration official said Ruckelshaus "didn't fully appreciate the opposition of Stockman to environmental programs" when he decided to return to the agency last year, although he knew there were limits on what he could accomplish.

Ruckelshaus was the EPA's first administrator, from 1970 to 1973. He was a vice president of Weyerhaeuser Corp., a major timber concern, when he took the EPA post last year.

Thomas was Ruckelshaus' choice as his successor because of his work as assistant EPA administrator in charge of hazardous waste, the prime national environmental problem. Thomas rebuilt the toxic waste cleanup program in the wake of scandals that forced the resignation of then-Administrator Anne M. Burford and two dozen other appointees in 1983.

Thomas said yesterday that he planned to continue Ruckelshaus' policies and agenda, adding that he expects he can defend the integrity of EPA's programs while also being an administration "team player." Environmentalists praised him, but also questioned whether he has the political clout to resist budget cuts and policy changes that could weaken environmental enforcement.

Sen. Robert T. Stafford (R-Vt.), chairman of the Environment and Public Works Committee that will handle Thomas' confirmation, yesterday praised him as "forceful and able" in running the hazardous waste cleanup program, and predicted that Thomas will be approved by the Senate.

White House sources said conservative Republicans, who had hoped to influence the choice of an EPA chief, were dismayed by the appointment of Thomas, a career bureaucrat and registered independent.