A method for manufacturing a silicon carbide semiconductor device includes the following steps. There is prepared a first silicon carbide layer having a first main surface and a second main surface. A first recess including a side portion and a bottom portion is formed in the first main surface of the first silicon carbide layer. A second silicon carbide layer is formed in contact with the first main surface, the side portion, and the bottom portion. An image of a second recess formed at a position facing the first recess of the fourth main surface is obtained. Alignment is performed based on the image of the second recess. The first main surface corresponds to a plane angled off relative to a {0001} plane. A ratio obtained by dividing a depth of the first recess by a thickness of the second silicon carbide layer is more than 0.2.