A method for manufacturing a silicon carbide semiconductor substrate is provided to offer a silicon carbide semiconductor substrate having a highly flat surface at low cost. The method includes: a step of preparing a silicon carbide substrate as a seed substrate; a step of performing vapor phase etching onto a main surface of the silicon carbide substrate; and a step of epitaxially growing silicon carbide on the main surface. A carbon-atom containing gas is supplied to silicon carbide substrate from a point of time in the step of performing the vapor phase etching.