Abstract: A substrate processing apparatus includes a substrate holding part configured to hold and support a substrate, a heating module configured to heat a substrate, and a cooling module configured to cool the substrate heated in the heating module. The substrate processing apparatus further includes a substrate transfer mechanism configured to take out the substrate from the substrate holding part and to sequentially transfer the substrate to the heating module and the cooling module, and a control unit configured to set a cooling time of the substrate in the cooling module based on a transfer history of the substrate while the substrate heated in the heating module is loaded into the cooling module.