The entrepreneur and his wife, Talulah Riley, issued a joint statement Wednesday announcing they are splitting amicably after they remarried in July 2013 following their previous breakup.
A spokeswoman says Musk filed for divorce on New Year's Eve and has agreed to give Riley $16 million in a financial settlement.
The couple first wed in 2010 and divorced in 2012. Musk announced the first divorce on Twitter.
Musk made his fortune co-founding PayPal and has gone on to start SpaceX and Tesla Motors.
The couple has been living apart for five months while Riley writes and directs her first feature film, Scottish Mussel, in the United Kingdom.
The spokeswoman says the two remain friends.