The United States ambassador in Moscow, Malcolm Toon, warned in a broadcast yesterday that a trial of jailed Soviet dissident Anatoly Scharansky would have a "very negative effect" on Washington's already "difficult" relations with the Kremlin.

"I think this is a very series question," Toon said in an interview taped in Moscow by the Voice of America, "and I think the Soviet side ought to look at it seriously."

Scharansky, a 30-year-old computer specialist, sought unsuccessfully to emigrate to Israel and was arrested a year ago after the Soviet press accused him of spying for the United States. President Carter hsas flatly denied the allegations. A trial of Scharansky, possibly on treason charges, could come at any time, according to reports from Moscow.

Toon who taped the interview with VOA correspondent Mark Hopkins last Firday, was also critical of the Soviet stance in the strategic arms talks with the United States as well as the Kremlin position in the Middle East and the Horn of Africa.

The ambassador's remarks were notable in several repects. Career diplomats such as Toon rarely speak so bluntly in public about the policies of governments to which they are accredited, particularly one as sensitive as the Soviet Union.

Moreover, Toon's comments on the Scharansky case amount to a prediction that the United States will respond sharply in other areas of U.S. Soviet relations should the trial go forth - the sort direct of "linkage" between issues administration spokesman had sought to avoid in the part.

"I think all of us that focuss on the relationship between Moscow and Washington," said Toon, "feel strongly that a Scharansky trial, and a brutal move against Scharansky, will have a very negative effect on our relations and it will make it very difficult indeed for us to do the sorts of things which I think both of us feel are essential to peace and stability in the world."

On SALT, Toon was critical of the Kremlin for blaming the United States exclusively in the Present stalmate.

"The Soviets," he said, "bear as much responsibility for the present situation as we do . . . For our part we continue to work and hope for a SALT treaty in the near future. But in all frankness, the process is not served by a campaign of threats and charges such as we see at the present time in the Soviet press."

He was referring primarily to a major article in the Communist Party newspaper Pravda last week warning of serious deterioration in Soviet-American relations if the U.S. does not accept a SALT accord.

Toon, has been in Moscow since the end of 1976, but his appointment was delayed for several months because of Soviet reluctance to accept him. Toon had served in the Soviet Union before and had never made a secret of his disapproval of Kremlin policies.