A method for controlling a temperature adjustment system of a machine tool is provided. With the method, a temperature rise value ΔTk of a main spindle device after stopping of rotation of a main spindle is obtained by using a reference temperature measured by a machine body temperature sensor mounted in a portion other than the main spindle device of a machine tool to calculate an estimated temperature yk. Therefore, as compared to a conventional method based only on a temperature of a cooling medium, supply of the cooling medium by a cooling device can be stopped or an operation of the cooling device can be switched from a first mode to a second mode without deteriorating machining accuracy in the main spindle device, thereby efficiently reducing power consumption.