The news about Davies' departure came as the upmarket chocolate company posted a profit warning, prompting its shares to tumble 12% to a nine-month low of 87.6p.
Thorntons said Davies had decided to step down to make way for someone with more experience in the retail side of the chocolate industry, which was proving more lucrative for the company.
For the past nine months, Thorntons had been experiencing a shift in sales pattern into supermarkets and away from its branded retail outlets, said a spokesman for the company.
While first-quarter sales through its own stores were down 4.9% this year, value sales of Thorntons products in other retailers were up a hefty 33.9%, according to the company's trading statement in April.
Davies had recognised someone with more experience dealing with supermarkets was more suited to the CEO role, said the spokesman.
"Thorntons shops have trodden water and experienced no growth, and after four years, Mike realises the company needs someone who has commercial supermarket experience. Retail is not his forte, and he would be first to admit that. He is very conscious that retail is the priority."
He added that Davies had "admirably and sensibly" decided to step down but would remain at the company and initiate the search for a successor with Thorntons chairman John von Spreckelsen, who is a former CEO at Somerfield.
Davies was appointed as CEO in 2006 following the resignation of Peter Burdon. Prior to joining, 53-year old Davies spent 20 years at Mars' chocolate division, where he held senior positions including managing director for UK and Ireland, European vice president for sales and most recently as president of Latin America. Before Mars, he spent three years with P&G.