According to one embodiment, there is provided a method for manufacturing a magnetic recording medium, the method including: depositing a magnetic recording layer on a substrate; forming a mask on a region of the magnetic recording layer corresponding to a recording area; irradiating another region of the magnetic recording layer where the mask is not formed with an ion beam using a C-containing gas as a source gas to deactivate the another region and to thereby form a non-recording area; and forming a protective film over an entire surface of the substrate.