A method of manufacturing a silicon carbide semiconductor device is disclosed in which a trench and a hole are controlled to have a predetermined configuration even if the silicon carbide semiconductor device is subjected to a heat treatment at a temperature of not lower than 1,500° C. A heat treatment step(s) of a method of the invention includes a step of heat treatment in an argon atmosphere at a temperature in a range of 1,600° C. to 1,800° C. under a pressure of at most 10 Torr for a time duration in a range of 0.1 min to 10 min to evaporate silicon atoms from a surface of the silicon carbide semiconductor substrate or the silicon carbide epitaxial layer and to obtain a silicon carbide surface with a carbon atom concentration of at least 95%. The method can further comprise a step of ion implantation of nitrogen ions or phosphorus ions in a dose amount of 8×1014 cm−2 into a surface of the silicon carbide semiconductor substrate or into the silicon carbide epitaxial layer, followed by the step of heat treatment at a temperature of 1,500° C. or higher. The method can comprise a step of heat treatment in an atmosphere of argon gas at a temperature in a range of 1,600° C. to 1,800° C. containing monosilane in an amount of at least 0.2%.