There are provided a method for manufacturing a magnetic recording medium which is excellent in terms of both the recording and reproduction characteristics and the thermal fluctuation characteristics without reducing the density and hardness of the perpendicular magnetic layer; a magnetic recording medium; and a magnetic recording and reproducing apparatus with which an excellent recording density is achieved,wherein, in the method for manufacturing the magnetic recording medium,at least a portion of the perpendicular magnetic layer 4 is formed as a magnetic layer having a granular structure that contains Co as a major component and also contains an oxide of at least one nonmagnetic metal selected from the group consisting of Cr, Si, Ta, Al, Ti, W and Mg;a target for forming the perpendicular magnetic layer 4 by the sputtering process is prepared so as to include an oxide of Co and a compound of Co and at least one nonmagnetic metal selected from the group consisting of Cr, Si, Ta, Al, Ti, W and Mg, and to make the proportion of oxygen contained in the target higher than the proportion of oxygen contained in the perpendicular magnetic layer 4; anda sputtering gas pressure at the time of forming the perpendicular magnetic layer is set to 1 Pa or less.