Timothy Naftali said he would be joining the New America Foundation think tank and completing a book on Nixon's political rival, John F. Kennedy.
His last day will be Nov. 19.
"I have much broader intellectual interests than Richard Nixon's presidency, and I'm going back to them," said Naftali, who oversaw the transfer of the Yorba Linda library from private hands to the federal government.
The Los Angeles Times said Saturday Naftali apparently ruffled some feathers among library supporters with his plans for a comprehensive exhibit on Watergate, which included a section with the unflattering title "Dirty Tricks and Political Espionage."
The Nixon Foundation objected to the wording of the display's text, which led to a nine-month delay in its opening. The Times said until Naftali arrived four years ago, Watergate was portrayed in line with Nixon's version of the scandal.