The disclosure is a thermal stability control system and a control method thereof for a machine tool. The control system mainly consists of a machine cooling sub-system composed of a pump, at least a cooling loop and a tank for storing cooling fluid, a cooling fluid cooling and heating sub-system, a heater and a micro controller. The cooling fluid cooling and heating sub-system further consists of a condenser, an evaporator, a directional valve, an expansion valve and a compressor. The micro controller dominates corresponding operation combinations of turning on/off the heater, enabling/disenabling the cooling fluid cooling and heating sub-system as a heat pump or a cooler by activating/releasing the directional vale, and adjusting upward/downward the driving frequency of an inverter duty motor to drive the pump to change the flow rate of cooling fluid through the cooling loop according the real time load of the machine tool.