A cleaning method of a silicon substrate includes a first step of etching a surface of a silicon substrate by a metal-ion-containing mixed aqueous solution of an oxidizing agent and hydrofluoric acid and of forming a porous layer on the surface of the silicon substrate, a second step of etching a pore of the porous layer by mixed acid mainly containing hydrofluoric acid and nitric acid and of forming texture on the surface of the silicon substrate, a third step of etching the surface of the silicon substrate on which the texture is formed with an alkaline chemical solution, and a fourth step of treating the silicon substrate etched by the alkaline chemical solution by ozone-containing water, of generating an air bubble within the pore formed in the silicon substrate, and of removing metal and organic impurities from within the pore.