A method of manufacturing a super-junction semiconductor device includes growing an alternating conductivity type layer epitaxially on a heavily doped n-type semiconductor substrate, the alternating conductivity type layer including n-type and p-type semiconductor regions arranged alternately and repeated such that n-type and p-type regions are adjoining each other, and arranged to extend perpendicular to the substrate's major surface. The method includes forming a first trench having a predetermined depth in the surface portion of n-type semiconductor region; forming an n-type thin layer on the inner surface of the first trench; and burying gate electrode in the space surrounded by the n-type thin layer with a gate insulator film interposed between a gate electrode and the n-type thin layer.