An object of the present invention is to provide a perpendicular magnetic recording medium 100 including a magnetic recording layer 122, the medium in which a particle diameter of crystal grains in the magnetic recording layer 122 of a two-layer structure is so designed as to improve an SNR while a high coercive force is maintained. In a method of manufacturing the perpendicular magnetic recording medium 100 according to the present invention, the perpendicular magnetic recording medium 100 includes at least a ground layer 118, a first magnetic recording layer 122a, and a second magnetic recording layer 122b in this order on a disk base 110; the first magnetic recording layer 122a and the second magnetic recording layer 122b are ferromagnetic layers each having a granular structure in which a grain boundary part made of a non-magnetic substance is formed between crystal grains each grown in a columnar shape, and A