The invention discloses a numerically-controlled machine tool temperature compensation system. The numerically-controlled machine tool temperature compensation system comprises a temperature difference calculation module, a deformation calculation module and a movement output module, wherein the temperature difference calculation module is connected with a machine tool numerical control system, acquires the motion state of a target movement shaft through the machine tool numerical control system and calculates the current temperature difference according to the motion state of the target movement shaft and the temperature difference calculation module, and the deformation calculation module is connected with the temperature difference calculation module and acquires the deformation amount of the target movement shaft according to the current temperature difference; the movement output module is connected with the machine tool numerical control system and the deformation calculation module, acquires the movement amount output by the machine tool numerical control system, and compensates for the movement amount according to the deformation amount so as to generate and output a movement target value. According to the numerically-controlled machine tool temperature compensation system, the deformation amount of a machine tool can be indirectly obtained through motion state by means of the temperature difference calculation module, and the motion state can be directly obtained through the machine tool numerical control system; therefore, the deformation amount of the machine tool can be calculated automatically and intelligently.