A method of manufacturing a semiconductor device includes: preparing a stepped structure being arranged on a substrate, the stepped structure including a first region and a second region, a height of the stepped structure of the second region being lower than a height of the stepped structure of the first region; and etching the first region and the second region of the stepped structure by irradiating the first region and the second region with an ion beam, an irradiation amount of the ion beam irradiating the first region is larger than an irradiation amount of the ion beam irradiating the second region.