A substrate processing apparatus includes a process container; a process gas supply mechanism; a substrate loading table; a temperature adjusting medium passage; a temperature adjusting medium extraction mechanism; a heater; and a temperature controller. The temperature controller is configured to adjust a temperature of a target substrate to a first temperature by allowing a temperature adjusting medium to flow through the temperature adjusting medium passage of the substrate loading table; and adjust the temperature of the target substrate to a second temperature higher than the first temperature by extracting the temperature adjusting medium of the temperature adjusting medium passage using the temperature adjusting medium extraction mechanism while heating the target substrate using the heater.