President Reagan accused the Soviet Union yesterday of "persecuting innocent people" by sharply curtailing the emigration of Soviet Jews to Israel, and warned that Moscow faces "the world's condemnation for making a mockery" of the Helsinki accords.

Speaking by telephone to the Anti-Defamation League of B'nai B'rith, Reagan said he was "very disturbed" by the assertion of a Soviet official this week that the majority of Soviet Jews who want to join families in Israel have left, and those who still want to go have become "victims of Zionist propaganda."

"Let us stand together, speak the truth and tell the Soviets, stop persecuting innocent people. Let Israel's children go, or face the world's condemnation for making a mockery of an historic agreement that was signed by 35 nations," Reagan said, to applause from the group.

He was referring to the 1975 Helsinki agreement in which the Soviets and other nations pledged to deal in a "positive and humanitarian spirit" with applications of persons who want to emigrate to be reunited with their families.

According to figures compiled by the National Conference on Soviet Jewry, Jewish emigration has declined from a peak of 51,320 in 1979 to 2,688 last year. So far this year, emigration has amounted to about 100 persons a month, according to the group. There are about 1.8 million Jews in the Soviet Union.

In his eight-minute talk to the Anti-Defamation League, Reagan directed harsh words at Moscow on other fronts as well. "It's no coincidence that the same forces which are destabilizing the Middle East--the Soviet Union, Libya, the PLO--are working hand-in-glove to destabilize Central America," he said."

Reagan was applauded for his pledge to stand by Israel and his comments on Soviet Jewry, but not when he appealed for support of "our friends" in Central America.

"The question isn't who has the most perfect democracy," Reagan said. "The question is who's trying to build democracy and who is determined to destroy it."

Apparently referring to complaints of widespread murders and human rights abuses by the U.S.-backed regime in El Salvador, Reagan said the United States had "once condoned slavery," but he said that many nations have "evolved into better democracies over time."

He added that "the nations which fall into the clutches of totalitarianism do not become free again."

The president, in response to a question about the prospects for Syrian withdrawal from Lebanon, said he remains "optimistic," and said that "I can't believe at this point . . . that it's all going to end here."

U.S. Ambassador to Israel Samuel W. Lewis offered a somewhat less upbeat view in a speech after Reagan's remarks. "I don't want to be a Pollyanna about the prospects," Lewis said of the Israeli-Lebanon peace accord that hinges on Syrian agreement to withdraw from Lebanon. "The chances of implementing it remain in the air."

Lewis said Israeli Prime Minister Menachem Begin will visit the United States in the next few weeks. After a period of strained U.S.-Israeli relations that he described as the worst since 1956 and the most difficult of his six years in the post, Lewis predicted that "the relationship is going to get better in the weeks and months ahead."