The Soviet Union has accepted an invitation from the United States for its new foreign minister, Eduard Shevardnadze, to meet with President Reagan and Secretary of State George P. Shultz in September, administration sources said yesterday.

Shultz is expected to meet Shevardnadze at the opening session of the U.N. General Assembly, officials said. Reagan has traditionally delivered an address at the United Nations, but a meeting between Shevardnadze and the president may be held at the White House, officials said.

Such a meeting would provide an opportunity to make substantial diplomatic preparations for the scheduled November summit between Reagan and Soviet leader Mikhail Gorbachev in Geneva. It would also come just as a third round of U.S.-Soviet nuclear arms talks are getting under way in Geneva.

Officials cautioned that a meeting with Shevardnadze would depend on the president regaining full health by September following his intestinal surgery last weekend. Doctors have predicted that Reagan will be back to normal by then.

An informed official pointed out that meetings between the U.S. president and former Soviet foreign minister Andrei Gromyko had been routine for many years. However, the practice was halted after the Soviet invasion of Afghanistan. Reagan held his first meeting with Gromyko -- now the Soviet president -- at the White House last fall after both delivered addresses at the United Nations.

White House spokesman Peter H. Roussel, asked for comment on a possible meeting between Reagan and the Soviet foreign minister, said last night, "We don't have any announcement to make at this time."

Reagan had invited Gorbachev to a meeting in the United States, but the Soviets sought a neutral site. A decision for Shevardnadze to meet Reagan at the White House could be a gesture by the Soviets in response to Reagan's original invitation.

Shultz and Shevardnadze are scheduled to hold their first meeting July 31 in Helsinki. Shevardnadze, previously the communist leader of the southern Soviet republic of Georgia, was elevated to foreign minister July 2, succeeding Gromyko, who held the post 28 years. Gromyko became Soviet president the same day.

A White House official, offering a modest goal for the Reagan-Gorbachev meeting, said yesterday Reagan hopes it will "set the agenda" for the next few years of U.S.-Soviet relations.

Edward P. Djerejian, the White House deputy press secretary for foreign policy, said that this agenda-setting, rather than any arms control agreement, is the "benchmark" that should be used to judge the meeting, which he declined to call a "summit."

Djerejian said the Reagan administration's view is that the first meeting of the two leaders should not have "an exclusive preoccupation with arms control, but it is obviously an important agenda item. We would hope that the Soviet Union would come prepared to inject momentum into the arms control process."

His comments came a day after U.S. and Soviet negotiators adjourned a second round of nuclear arms talks in Geneva without signs of progress.

Some U.S. officials are hoping that the Reagan-Gorbachev meeting, scheduled to begin shortly after the third round of talks conclude, will give impetus to the arms control negotiations.

But U.S. officials have been trying to keep expectations for the summit meeting at a low level, avoiding the thorny issue of the Reagan missile defense plan formally called the Strategic Defense Initiative and commonly known as "Star Wars."

The Soviets have called upon the United States to abandon this initiative, which has been strongly pushed by Reagan.

Shevardnadze's acceptance of the invitation to meet with Reagan and Shultz was first reported last night in The Boston Globe.