Chief Justice William H. Rehnquist threw his weight Sunday behind an effort to boost federal judges' salaries by 51 percent to $135,000 a year.

Rehnquist, in his 1988 year-end report on the federal judiciary, strongly endorsed a presidential commission's recommendation of hefty pay raises for judges and about 2,000 other top federal officials.In addition to calling for the big pay raise for the trial judges, who now make $89,500, the commission recommended boosting salaries of federal appeals court judges from $95,000 to $140,000, a 47 percent jump; of Supreme Court associate justices from $110,000 to $165,000, a 50 percent increase; and of the chief justice from $115,000 to $175,000, a 52 percent increase.

The recommendations are pending before President Reagan, who can accept or modify the figures before sending his fiscal 1990 budget to Congress on Jan. 9.

Under the law, whatever pay increases the president endorses will take effect 30 days later unless both the House and the Senate vote to set them aside.