A manufacturing method of a semiconductor substrate includes: forming a trench in a semiconductor board by a dry etching method; etching a surface portion of an inner wall of the trench by a chemical etching method so that a first damage layer is removed, wherein the surface portion has a thickness equal to or larger than 50 nanometers; and performing a heat treatment at temperature equal to or higher than 1050° C. in non-oxidizing and non-azotizing gas so that crystallinity of a second damage layer is recovered, wherein the second damage layer is disposed under the first damage layer. The crystallinity around the trench is sufficiently recovered.