Merrill, a former Google chief information officer whose arrival at EMI in April last year was heralded with much fanfare, was one of the highest profile hirings made by EMI. It is not known whether he has a job to go to.
EMI has not elaborated on the reasons for his departure, but the since his arrival it has continued to struggle to transform its business model from one based on traditional music formats such as CDs and vinyl to one based on digital.
A week ago, Guy Hands, the chief executive of EMI parent Terra Firma Capital Partners, resigned from his day-to-day leadership of the venture capitalist group, which recently wrote off €1.3bn (£1.19bn) of its investment in EMI.
At the time of Merrill's appointment, it was clearly hoped that he would preside over a transformation of the business. However, developments such as a dedicated website selling music to consumers have failed to spark demand.
Elio Leoni-Sceti, EMI chief executive, : "Douglas Merrill has today stepped down from his roles as president of digital and [chief operating officer] of EMI New Music and will be leaving the company.
"I would like to thank Douglas for his contribution and to wish him well for the future."
Merrill's responsibilities will be taken on by his number two, Cory Ondrejka, who is promoted to the newly created position of executive vice-president of digital marketing.
Ondrejka, one of the founders of virtual world Second Life, joined EMI last summer as senior vice-president of digital strategy.