The present invention provides a method of manufacturing a magnetic recording medium where at least a magnetic layer is formed on a non-magnetic substrate and a magnetically separated magnetic recording pattern is formed on the magnetic layer, including: a magnetic recording pattern forming process of forming magnetic recording areas that are constructed with convex portions and boundary areas that are constructed with concave portions between the magnetic recording area as the magnetic recording pattern on the magnetic layer; followed by a protective layer forming process of forming a protective carbon layer by using a high-frequency plasma chemical vapor deposition method and by applying a negative bias to the non-magnetic substrate to make the protective carbon layer on the magnetic recording area thinner than the protective carbon layer on the boundary area.