A substrate processing apparatus includes: a processing container, a temperature adjustment furnace, and a controller. The temperature controller includes at least one of a ceiling heater heating the processing container from a ceiling and a lower heater heating a portion below the processing container. The controller calculates a temperature condition for each of the plurality of zones to uniformize a film thickness among the plurality of substrates during the substrate processing, by using a retained upper-portion temperature model and/or lower-portion temperature model, acquires the film thickness of the plurality of substrates when the substrate processing is performed under the calculated temperature condition, and compares the acquired film thickness with a target film thickness, and when the acquired film thickness falls outside an allowable range of the target film thickness, sets a process region to be applied to the substrate processing on the plurality of substrates, based on the comparison.