A manufacturing method of a silicon carbide semiconductor device includes: forming a drift layer on a silicon carbide substrate; forming a base layer on or in a surface portion of the drift layer; forming a source region in a surface portion of the base layer; forming a trench to penetrate the base layer and to reach the drift layer; forming a gate electrode on a gate insulation film in the trench; forming a source electrode electrically connected to the source region and the base layer; and forming a drain electrode on a back surface of the substrate. The forming of the trench includes: flattening a substrate surface; and etching to form the trench after flattening.