The cover on the magazine's July 24 issue features an image of Trump Jr., with excerpts from the emails he made public on Tuesday superimposed on the photo, reports CNN.
The emails show that Trump Jr. agreed to meet with someone who was a "Russian government attorney" about "very high level and sensitive information" that would "incriminate" the former presidential hopeful.
Time's title: "Red Handed", written by Time editor-at-large David Von Drehle, explores what kind of damage the email story might cause for Trump Jr. and his father's presidency.
President Donald Trump has had a longtime preoccupation with Time covers. He was first featured on the magazine in 1989, and he called it a "very, very great honour" last year when he was named its Person of the Year, CNN reported.
Trump even bragged during a speech at the CIA headquarters in January about his cover count: "I think we have the all-time record in the history of TIME magazine."
Trump's fascination with the magazine has sometimes manifested itself in strange ways. Last month, The Washington Post reported that a faked TIME magazine cover featuring Trump had been framed and hung up in at least five of Trump's clubs.
After the story was published, TIME asked the Trump Organization to remove the Photoshopped covers.