According to one embodiment, there is provided a method of manufacturing a magnetic recording medium, including forming a first hard mask including carbon as a main component, a second hard mask including a main component other than carbon and a resist on a magnetic recording layer, contacting a stamper to the resist to transfer patterns of protrusions and recesses to the resist, removing residues in the recesses of the patterned resist, etching the second hard mask, etching the first hard mask, patterning the magnetic recording layer, and removing the first hard mask, the method further including, between etching the first hard mask and removing the first hard mask, removing the second hard mask remaining on the protrusions of the first hard mask, and removing a contaminating layer on a surface of the first hard mask by a mixed gas of oxygen-based gas and a fluorine compound.