A method of manufacturing a silicon carbide semiconductor device includes forming a constituent layer and forming a super junction structure. The formation of the super junction structure includes forming a film-forming mask on the constituent layer, forming an opening portion at the film-forming mask, forming a mask-forming trench at the constituent layer and adopting a portion of the constituent layer surrounding the mask-forming trench as a silicon carbide mask through etching by adopting the film-forming mask, forming a second-conductivity-type column region by ion implantation of impurities at a bottom surface of the mask-forming trench by adopting an ion-implantation mask having the film-forming mask and the silicon carbide mask, and removing a portion of the constituent layer where the silicon carbide mask is formed.