Mercedes chief designer John Irving will leave the team later this year.
The 52-year-old has been a key figure in Brawn’s 2009 and 2010 Mercedes championship successes since joining Honda in 2007.
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Brawn won the drivers’ and constructors’ titles from 2014-21, before Mercedes won seven drivers’ titles and eight constructors’ titles.
A statement from Mercedes said Owen would leave “after ensuring the transition to his successor” and then take a period of gardening leave.
There is no information on what the next step in his career might be.
Engineering director Giacomo Tortora will serve as vehicle design director, the team said, with the team led by deputy technical director Simone Resta.
Owen worked for the Swiss Sauber team and became senior aerodynamicist in 2004 before switching to Honda. He began his career at the now-defunct racing car manufacturer Reynard.
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