Khalil Lee’s time with the Mets is over.

The team released the 24-year-old outfielder on Sunday, The Post confirmed.

Lee, who was with Triple-A Syracuse, had been designated for assignment and removed from the 40-man roster in February while under MLB investigation involving allegations that he assaulted his former girlfriend in May 2022, while also playing for Syracuse.

He was accused in a lawsuit of choking the woman and kicking her to the ground.

Lee remained with the organization after clearing waivers in February and was signed to a minor league contract.

He struggled in 21 games with Syracuse this season, with a .621 OPS in 77 plate appearances.

A source said the decision to cut ties with Lee was “baseball-related.”

Lee appeared in 13 games with the Mets from 2021 to 2022 and went 2-for-20 with a homer, a double and 13 strikeouts.