According to one embodiment, a method of manufacturing a magnetic recording medium includes forming a resist on a magnetic recording layer, imprinting a stamper to the resist to transfer patterns of protrusions and recesses, and partially etching the magnetic recording layer in areas not covered with patterns of the resist used as masks by ion beam etching using a mixed gas of He and N2 as well as modifying a remainder of the magnetic recording layer to leave behind a nonmagnetic layer having a reduced thickness.