Preston formerly worked at the The Times for 15 years as deputy editor, a title he left in 2008.
The move comes as the newspaper prepares to redesign later this month.
Bob Tyrer will remain as an executive editor alongside Ben Preston.
Martin Ivens, editor of The Sunday Times, said: "Ben is a hugely respected and versatile editor, able to combine incisive news judgment with a flair for engaging features, investigations and campaigns. His breadth of experience, across both newspapers and magazines, is a perfect match for The Sunday Times and I am delighted that he will be bringing his many talents to the paper."
Preston said: "The Sunday Times has been breaking great stories and leading investigations throughout my life in journalism. It’s a privilege now to be joining The Sunday Times and having this opportunity to continue that great tradition both in print and in pixels. News has always been my first love and with Brexit and Trump I can’t think of a more exciting time to be working for ‘the’ Sunday newspaper with such a hugely talented team."