The company said Friday that current President Baxter Phillips will replace Blankenship.
Blankenship, who joined the central Appalachian coal producer in 1982, said it was time to go after nearly 30 years with the company.
The southern West Virginia native's tenure with Massey has been marked by battles with labor and government regulators.
He is currently fueding with the federal Mine Safety and Health Administration over safety issues at the company's Upper Big Branch mine. An explosion at the mine in April killed 29 and injured two.
Blankenship has blamed the explosion on a sudden rush of natural gas into the mine, and ventilation changes forced by MSHA.