According to one embodiment, a method of manufacturing a magnetic recording medium includes forming a first hard mask, a second hard mask and a resist on a magnetic recording layer, imprinting a stamper to the resist to transfer patterns of protrusions and recesses to the resist, removing residues remaining in the recesses of the patterned resist by means of a first etching gas, etching the second hard mask by means of the first etching gas using the patterned resist as a mask to transfer the patterns to the second hard mask, etching the first hard mask by means of a second etching gas different from the first etching gas using the second hard mask as a mask to transfer the patterns to the first hard mask, and performing ion beam etching in order to deactivate the magnetic recording layer exposed in the recesses and to remove the second hard mask.