To provide a magnetic recording medium enabling excellent magnetic recording reproduction characteristics to be exhibited with the spacing loss reduced and a manufacturing method of the medium, a method of manufacturing a magnetic recording medium of the invention is to manufacture a magnetic recording medium having a magnetic recording layer of a granular structure having nonmagnetic boundary portions between pillar-shaped magnetic particles on a nonmagnetic substrate, and an exchange coupling layer provided on the magnetic recording layer to add an action of exchange coupling the magnetic particles, and is characterized by having an ion irradiation step of performing ion irradiation on the entire surface of the exchange coupling layer after layering the exchange coupling layer on the magnetic recording layer.