In this method for manufacturing a semiconductor element, a modified layer produced by subjecting a substrate (70) to mechanical polishing is removed by heating the substrate (70) under Si vapor pressure. An epitaxial layer formation step, an ion implantation step, an ion activation step, and a second removal step are then performed. In the second removal step, macro-step bunching and insufficient ion-implanted portions of the surface of the substrate (70) performed the ion activation step are removed by heating the substrate (70) under Si vapor pressure. After that, an electrode formation step in which electrodes are formed on the substrate (70) is performed.