The Fast & Furious director will succeed Roberto Orci, who will remain as a producer on the movie.
Lin was the only person offered the job although numerous filmmakers were in contention, according to Deadline.
Edgar Wright, Rupert Wyatt and Duncan Jones were among those tipped for the director’s chair on Star Trek 3, along with Morten Tyldum (The Imitation Game) and Daniel Espinosa (Safe House).
Lin’s involvement has been made possible as his planned Bourne Legacy sequel with Jeremy Renner has been delayed following Matt Damon’s return to the spy series.
He is expected to start work on Star Trek 3 after his commitments to season two of True Detective are complete.
JJ Abrams elected not to direct Star Trek 3 in order to focus on Star Wars: The Force Awakens, and will be an executive producer on the sequel to Star Trek Into Darkness.
Chris Pine, Zoe Saldana, Zachary Quinto, Simon Pegg, Karl Urban, Anton Yelchin and John Cho are all expected to return for Star Trek 3, which is tipped for release in 2016.
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