A thermal compensation control system for a machine tool having a milling cutter and a cutter driver includes a tool setting probe, a temperature sensor, a workpiece touch probe, and a controller. The cutter driver is connected to the milling cutter to drive the milling cutter to process the work piece based on a control signal. The tool setting probe is configured to detect a cutter length of the milling cutter. The temperature sensor is configured to sense a measured temperature of the cutter driver or the milling cutter. The workpiece touch probe is configured to measure processing errors of the processed work piece. The controller is configured to generate the control signal based on a processing instruction, a temperature compensation model, the cutter length, and the measured temperature. The controller is further configured to determine whether to modify the temperature compensation model based on the processing errors.