Yelena Bonner, wife of Soviet dissident Andrei Sakharov, met this week with national security affairs adviser John M. Poindexter at the White House, but President Reagan decided not to see her out of concern that such a meeting could upset efforts to win freedom for others, administration officials said yesterday.

The meeting with Poindexter was "cool and correct," according to an informed source. "She was not happy." Another source said Bonner was told Reagan decided not to see her out of fear that if he did, the Soviet authorities might be tempted to deny her reentry to the Soviet Union.

She has been in this country since December for medical treatment, including a heart-bypass operation, but plans to return in May to the provincial city of Gorki, where Sakharov has been in forced exile since 1979.

An official familiar with Bonner's meeting with Poindexter said the National Security Council adviser stressed Reagan's concern about Sakharov's situation and about human rights in the Soviet Union. But, this official added, "We continue to believe that we should pursue these concerns through confidential diplomatic channels."

A White House official said, "There was talk about her meeting with the president. Reagan's attitude was that these are people I respect. But he doesn't want to do anything to lessen the chances of others being released. He's told a lot of people that he doesn't want to rock the boat."

In May 1976, Reagan sharply attacked then-President Gerald R. Ford for refusing to meet another prominent Soviet dissident, writer Alexander I. Solzhenitsyn. Reagan accused the Ford administration of "snubbing" Solzhenitsyn, and attacked Ford's secretary of state, Henry A. Kissinger. Reagan said Kissinger "felt such an offering of White House hospitality might be displeasing to the Kremlin."

Reagan continued to be an open and harsh critic of Soviet human-rights policies after he became president, but shifted his approach before last year's summit meeting with Gorbachev. In preparing for the summit, Reagan accepted the advice of former president Richard M. Nixon and others that he use "quiet diplomacy" rather than public criticism to encourage the Soviets to improve human-rights practices and permit greater emigration.

Yesterday, a White House official quoted Reagan as saying that he told Soviet leader Mikhail Gorbachev last year in Geneva that "we want to get people out of there, and if it happens we won't make a big to-do out of it. That's the message he wants to send: 'If you let the people go, we won't send out a press release.' "

Since the summit, Reagan has stuck with a low-key approach, recalling to aides that it was successful in efforts to win the release of a family of religious dissidents who spent five years in the basement of the U.S. embassy in Moscow. The Soviets also recently released dissident Anatoly Shcharansky, who immigrated to Israel after serving nine years in Soviet prisons.

Administration sources said yesterday they think that further releases may be forthcoming.

Sakharov, winner of the Nobel Peace Prize in 1975 for his supoprt of human rights, was a top physicist and helped develop the Soviet hydrogen bomb. He became a political dissident in the late 1960s before being ordered to internal exile in Gorki. Reagan issued a prolamation creating a national Andrei Sakharov Day on May 21, 1983, Sakharov's 62nd birthday.

Gorbachev recently told the French Communist Party newspaper L'Humanite that Sakharov "still has knowledge of secrets of special importance to the state, and for this reason cannot go abroad."

In a letter recently smuggled to the West, Sakharov said he was drugged, strapped down, force-fed and mentally tormented by KGB agents and state doctors seeking to end the hunger strike he launched in 1984 on behalf of his ailing wife. In other communications, Sakharov has said that he and Bonner have been held in total isolation in Gorki.

As a condition of her permission to travel here for medical care, Bonner promised the Soviet authorities in writing to give no news conferences or interviews in this country. She is still undergoing medical treatment and is scheduled to have an operation in Boston today to open a clogged artery in her leg. Staff researcher James Schwartz contributed to this report.