Disclosed are a substrate processing apparatus, a substrate processing method and a storage medium, capable of removing contaminant materials from a substrate by using SPM liquid (sulfuric acid and hydrogen peroxide mixture) while preventing degradation of the function of the SPM liquid for removing the contaminant materials. The SPM liquid is filled in a processing bath and the substrate is immersed in the SPM liquid. A heating unit is provided in the circulation path to heat the SPM liquid. A hydrogen peroxide supply line supplements hydrogen peroxide to the SPM liquid in the circulation path. A control unit adjusts the temperature of the SPM liquid to the predetermined temperature in the range of 135° C. to 170° C. based on a temperature detection value and outputs a control signal to supplement the sulfuric acid to compensate for the SPM liquid as the SPM liquid is evaporated by heating.