A substrate processing apparatus includes a first chamber, a second chamber which has a first valve, a second valve and a chuck, wherein a substrate is transferred to the second chamber through the first valve, held by the chuck in the second chamber, and then transferred to the first chamber through the second valve, a pressure reduction section which reduces a pressure in the second chamber to a predetermined pressure while the substrate is held by the chuck in the second chamber, a thermoregulator which is arranged in the chuck and regulates a temperature of the substrate held by the chuck to be a predetermined temperature, and a controller which controls the pressure reduction section so as to make a relationship between the pressure in the second chamber and a pressure reduction time in the second chamber fall within a predetermined range, controls the chuck so as to make a suction force for the substrate constant, and controls the thermoregulator so as to make a temperature of the chuck constant.