US media suggests Disney does not want to be associated with the media mogul's highly partisan, right-wing Fox News network.
However, Disney has not clarified its reasons.
It bought the studio, with other media operations, in a $71bn deal last March.
20th Century Fox is known for producing some of the biggest films of all-time, including Avatar and Titanic.
Hollywood is known for being liberal, unlike the Australian tycoon.
Disney has also renamed Fox Searchlight Pictures, the arthouse arm, as simply Searchlight Pictures.
Staff emails were changed on Friday, from @fox.com to @20thcenturystudios.com or @searchlight.com.
The original 20th Century Fox company was formed in 1935 following a merger.
Rupert Murdoch's News Corporation bought it in the mid-1980s, and the Fox News channel was created in 1996, growing to become most-watched in the US.
News Corporation was later split into News Corp and 21st Century Fox - which Disney acquired as the parent company of various film and television studios, including the renowned 20th Century Fox.
The Murdoch family retained the news outlets in a spin-off company, Fox Corporation, which is run by Rupert Murdoch's son Lachland.