Hart fills the gap left by former chief executive Mike Davies who stepped down in May after the chocolate maker issued a profit warning to the stock market.
Hart was executive director at Caffe Nero for just 18 months before a management buy-out in 2007, when he moved to the post of managing director. Under his tenure, store numbers doubled to more than 400 and his appointment hints at ambitious expansion plans for the company.
Thorntons said Hart streamlined Nero's product lines and increased profitability.
Chairman of Thorntons, John von Spreckelsen, said: "Jonathan brings a wealth of relevant experience to Thorntons from the retail and consumer goods sectors.
"He has an impressive track record in successfully running a number of multi-channel businesses, including concessions, and a proven track record in the development of retail format strategies, as well as new product development and launches. We are delighted that Jonathan has agreed to join Thorntons."
Prior to Caffe Nero, Hart worked for a variety of high-street names including Abbey, Woolworths, Big W and ITM Communications. He also worked for a decade at electrical group Dixons, where he was group managing director of both the high-street brands Dixons, The Link and Dixons Tax Free, and of PC World International.