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 film on a magnetic recording layer, imprinting a stamper on the resist film to transfer patterns of recesses and protrusions, removing residues remained in recess of the patterned resist film, etching the second hard mask using the patterned resist film as a mask to transfer patterns of recesses and protrusions, etching the first hard mask using the patterned second hard mask as a mask to transfer patterns of recesses and protrusions, and deactivating magnetism of the magnetic recording layer exposed in the recesses together with removing the second hard mask by ion-beam etching.