Jonathan Daniels, the former editor of The Raleigh (N.C.) News and Observer who served as press secretary to President Franklin D. Roosevelt and was an adviser to President Truman, died yesterday in Hilton Head Island, S.C., after a long illness. He was 79 years old.

Mr. Daniels was also a prolific author, a consummate politician, a historian, a gourmet and a gadfly. It was he who disclosed that President Roosevelt had a love affair with his wife's former social secretary, Lucy Page Murcer. Mr. Daniels wrote briefly about the affair in 1954 in his book ''The End of Innocence.'' And he gave the details of the relationship in his 1966 book ''The Time Between the Wars.''

Born in a rambling manor in Raleigh on April 26, 1902, Jonathan Worth Daniels was the son of a famous Southerner, Josephus Daniels, who was Secretary of the Navy under Woodrow Wilson, Ambassador to Mexico for nine years under Roosevelt and editor and publisher of The News and Observer in the early part of the 20th century. Famous Father and Son

Although he was born in the shadow of his famous father - Josephus Daniels gave President Roosevelt his first national exposure by hiring him as Assistant Secretary of the Navy - Jonathan Daniels went on to become famous in his own right, first as a reporter and writer, then as a public servant, a Tarheel politician with national connections and as a nationally respected newspaper editor.

Mr. Daniels grew up in Washington, D.C., in the hectic days before and during World War I. He returned to North Carolina after World War I to attend the University of North Carolina at Chapel Hill, where he was a classmate of Thomas Wolfe.

In 1921, Mr. Daniels got a B.A. degree. A year later he was awarded an M.A. at Chapel Hill. In 1922-23, he attended law school at Columbia University.

On Sept. 5, 1923, the young lawyer, who never practiced although he was admitted to the North Carolina bar, married Elizabeth Bridgers, of Raleigh.

After several months as a reporter for The Louisville Times, Mr. Daniels returned to Raleigh to work for his father. Started as a Police Reporter

He started as a police reporter but was made the paper's Washington correspondent in 1925, a job he left in 1928 to write his first novel, ''Clash of Angels,'' which he described as an allegorical fantasy concerning Jehovah and Lucifer.

In 1931, Mr. Daniels, whose wife died in 1929, leaving him with a daughter, joined Fortune magazine. He also won a Guggenheim fellowship for his novel and used that money to live in France and Italy while working on another novel that was never published.

In 1932, he married Lucy Cathcart, who died in 1979. Raleigh beckoned him once more in 1932, and he joined the News and Observer as associate editor. He became the editor a year later, when his father was appointed Ambassador to Mexico.

He remained editor until 1942, when President Roosevelt persuaded him to join the war effort in Washington as assistant director of the Office of Civil Defense.

A year later, the President appointed Mr. Daniels as his administrative assistant, and in 1945 the writer became the President's press secretary. After Roosevelt's death that year, he became a close adviser to President Truman.

Mr. Danels had a reputation in the South as a liberal, having spoken out against discrimination in that region for decades. He returned to Raleigh in 1947 to become executive editor of The News and Observer and the Democratic National Committeeman for North Carolina. Helped Truman in Campaign

But in 1948 President Truman called the editor back to Washington to help him run for re-election, and Mr. Daniels took the post of editor emeritus of his favorite newspaper.

Mr. Daniels retired from The News and Observer in 1970, but laterfounded The Island Packet newspaper on Hilton Head and started to write urbane, anecdotal and ironic columns for it.

Mr. Daniels is survived by four daughters, Elizabeth Squire of Weaverville, N.C.; Dr. Lucy Inman of Raleigh; Adelaide Key of Franklin, N.C., and Cleves Weber of New York City; a brother, Frank A. of Raleigh, chairman of the board of The News and Observer Publishing Company, 11 grandchildren and several great-grandchildren.

Funeral services will be held at 11 A.M. Monday at St. Luke's Episcopal Church at Hilton Head.