The Portadown driver leaves the team after two successful years, winning nine races and picking up 18 podiums.
The 34-year-old claimed a fifth independents championship win in 2015 driving a Volkswagen CC.
The team switched to a Subaru Levorg in 2016 and Turkington came close to securing a third BTCC title last year.
The Northern Irishman missed out in the final round at Brands Hatch despite being a rank outsider heading into the finale.
"I have thoroughly enjoyed my time at BMR, however, the time has come to part company and apply focus to each of our own individual goals and needs," said Turkington.
"I sincerely value the journey we have shared together securing the Teams Championship in 2015, winning my fifth Indy title and of course the thrilling year we have just had."
Turkington picked up the BTCC title in 2009 and in 2014, driving for WSR, before moving to BMR at the beginning of 2015.
He had a strong debut campaign with the team, however he starred in 2016, nearly winning the title despite an uncompetitive start to the year due to teething problems with the Levorg.
Turkington is expected to stay in the BTCC in 2017, with several front running seats still available.
Double British Touring Car Championship winner Colin Turkington has announced his departure from Team BMR ahead of the upcoming season.