According to one embodiment, a method of manufacturing a magnetic recording medium includes forming a hard mask and a resist on a magnetic recording layer, imprinting a stamper on the resist to transfer patterns of protrusions and recesses, removing resist residues left in the recesses of the patterned resist, etching the hard mask using the patterned resist as a mask to transfer the patterns of protrusions and recesses, stripping the resist, and performing ion beam etching to remove the remaining hard mask and to modify a surface of the magnetic recording layer uncovered with the remaining hard mask.