The appointment marks the first time that the UK record label has created such a post.
Merrill, who oversaw Google's successful stock market listing in 2004, will start his new role of beefing up EMI Music's online operations on 28 April at the firm's Los Angeles office.
Guy Hands, chief executive at Terra Firma, and chairman of EMI Group, welcomed the new online boss, praising his business intellect and engineering expertise.
"Merrill's experience, talents and ability to drive innovation will be enormously valuable to EMI and its artists," said Hands.
Merrill explained in a statement that the new post will allow him to combine two of his biggest passions.
"One is creating platforms and tools that make it easier for consumers to achieve their goals. The other is music," he said.
"This exciting new role at EMI is a unique opportunity for me to put those two passions to work together, and help deliver EMI's objective of providing the best services in the world to consumers and musicians."
Merrill's move to EMI follows last month's high-profile departure of Sheryl Sandberg, Google's vice president of global online sales, to become the new chief operating officer at Facebook.
Another departure saw Ethan Beard quit as head of social media at Google to join Facebook as director of business development.
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