Provided are a substrate processing apparatus, a semiconductor device manufacturing method, and a temperature controlling method, which are adapted to improve equipment operational rate. A calculation parameter computing unit computes a calculation parameter using at least a first calculation parameter correction value determined by a first calculation parameter setting unit based on an accumulated film thickness on a reaction vessel, a second calculation parameter correction value determined by a second calculation parameter setting unit based on an accumulated film thickness on a filler wafer, and a third calculation parameter correction value determined by a third calculation parameter setting unit based on the number of filler wafers. Product and filler wafers are accommodated and heat-treated in the reaction vessel while controlling a heating unit using calculation results obtained using at least the calculation parameter and deviation between a set temperature and a temperature detected in the heating unit by a temperature detector.