The present invention provides a magnetic recording medium capable of recording or reproducing high-density information by reducing the grain size of a perpendicular magnetic recording layer and improving vertical orientation, a method of manufacturing the same, and a magnetic recording/reproducing apparatus. The perpendicular magnetic recording medium includes: a non-magnetic substrate; and at least an soft magnetic layer, an under layer, an intermediate layer, and a perpendicular magnetic recording film that are formed on the non-magnetic substrate. At least one layer of the intermediate layer is made of an alloy material of an element having an fcc structure and an element having a bcc structure or an hcp structure, and has both a crystal structure having (111) orientation and an irregular layer lattice (stacking fault) caused by a mixture of the fcc structure and the bcc structure. The at least one layer of the intermediate layer is made of an alloy material of at least one element that is selected from a group composed of Pt, Ir, Pd, Au, Ni, and Co, which is a main ingredient, and has the fcc structure, and an element having the bcc structure or the hcp structure.