Wilson (pictured), a long-time ally of M&S chief executive Stuart Rose, will leave the retailer on October 28 to join Booker Cash and Carry as chief executive.
He is staying on at M&S to allow new group finance director Ian Dyson time to fully settle in.
M&S said that Wilson will not be replaced and his roles will be reallocated to other executives in due course.
Rose said: 'Charles joined to do a specific job, namely to help focus the business and to deliver cash and cost improvements. He has delivered these and helped build a solid foundation for the company to go forward.'