Clement R. Haynsworth Jr., a respected Southern jurist who was rejected as Richard Nixon's nominee to the Supreme Court nearly 12 years ago, said yesterday he will retire as chief judge of the 4th U.S. Circuit Court of Appeals, effective April 6.

Haynsworth, whose decision surprised court colleagues, said yesterday he intends to keep a full and active schedule as a senior judge on the panel -- something permitted under the retirement rules -- relinquishing only his administrative duties. He has been head of the Richmond-based court for 16 of his 24 years on the appellate bench.

"I don't intend to stop working at all," Haynsworth, 68, said in a telephone interview from his office in Greenville, S.C. "It's just that the administrative detail has grown so much that it demands a substantial amount of my time away from hearing cases and writing opinions. I think I have borne the burden of chief judge long enough."

Haynsworth said he "made up my mind only about a week ago" to step down as chief judge of the 10-member court, which encompasses Virginia, West Virginia, Maryland, North Carolina and South Carolina. He informed President Ronald Reagan of his decision in a letter delivered to the White House yesterday afternoon. The Republican president is expected to fill the court vacancy with someone from Haynsworth's home state.

A shy, courteous and conservative jurist, Haynsworth found his rejection by the Senate as a Supreme Court nominee in 1969 especially painful.

The notoriety surrounding that rejection nearly shredded his judicial reputation.

During the hearings before the Senate Judiciary Committee, Haynsworth was attacked as anti-labor, called a "laundered segregationist" and accused of "ethical insensitivity" because he ruled in some cases in which he had a small financial link through stock holdings.

In the years since, however, even liberal law professors have praised his judicial abilities, accusing the Senate of giving him "a bum rap" in an attempt to strike out at Nixon.

Haynsworth, in a rare public comment on the controversy, told the Washington Post in 1979 that he had always regarded the Supreme Court flap as political. But, he said firmly, "I survived it."

Returning to his chief judge duties at the 4th Circuit, considered one of the most conservative in the nation's federal appellate system, Haynsworth guided his court through many controversial civil rights and labor law cases and a landmark decision on behalf of prisoner rights. The court also ultimately upheld the mail fraud conviction of former Maryland governor Marvin Mandel and five codefendants.

Haynsworth's replacement as chief judge will be Judge Harrison L. Winter of Baltimore, who has been a member of the court for 15 years and is considered a more liberal jurist than his predecessor.

Haynsworth pointed out yesterday that under federal law he would have had to step down as chief judge in October 1982 when he becomes 70. By announcing his retirement now, Haynsworth said, he gets to return to his preferred court duties and the 4th Circuit gets the needed services of another full-time judge.

As a senior judge, he will not be counted as part of the court's full complement of 10 active judges.

"So many of the district judgeships are being filled," Haynsworth said. "When they get in place, that will cut into their case backlog, and the number of appeals to my court will go up substantially."