A method of manufacturing a semiconductor device includes a semiconductor region forming process, a cleaning process, a surface roughness uniformizing process, and an electrode forming process. As the semiconductor region forming process, semiconductor regions are formed such that a plurality of semiconductor regions with different ion injection amounts are exposed on one principal surface of a semiconductor substrate. As the cleaning process, after the semiconductor region forming process, a cleaning using hydrofluoric acid is performed on the one principal surface of the semiconductor substrate. As the surface roughness uniformizing process, after the cleaning process, the surface roughness of the one principal surface of the semiconductor substrate is uniformized. As the electrode forming process, after the surface roughness uniformizing process, electrodes are formed on the one principal surface of the semiconductor substrate.