In a method of manufacturing a silicon carbide semiconductor device, a trench and a thickness measurement section are formed in a surface of a semiconductor substrate made of silicon carbide. The thickness measurement section includes a plurality of grooves and a protruding portion provided between the grooves so as to have a predetermined width. When an epitaxial layer made of silicon carbide is grown, a thickness of the epitaxial layer formed on the surface of the semiconductor substrate is measured by calculating a difference in height between a surface of the epitaxial layer formed on a portion of the surface of the semiconductor substrate different from the thickness measurement section and a top surface of the protruding portion. The predetermined width is less than a surface migration amount of atoms during growth of the epitaxial layer.