This invention provides a temperature control method, which includes the following steps: setting expected temperature value of circulating cooling temperature of temperature control system's output; according to the deviation between the current temperature in the circulating cooling liquid export and the expected value, adjusting power outputs of heating module and cooling module, and controlling the variation of temperature; dividing the change process of controlled temperature into three stages, the three stages are M1, M2 and M3, wherein, the M1 stage is used for improving response speed of the temperature control system, and approaching the expected the temperature value rapidly; the M2 stage is used for controlling slope of temperature change; the M3 stage is used for stabling system current temperature at the expected temperature. This invention provides a temperature control method and temperature control system thereof which divides the change process of controlled temperature into several stages, thereby causing the circulating cooling temperature up to the set point rapidly and improving the precision of control temperature.