Thermoelectric cooler was used as the main component of temperature controlling in hot embossing device to acquire high temperature control precision. The control model of thermoelectric cooler was derived by using small-signal linearization method due to its complex thermoelectric performance. A fuzzy PID controller is designed by combined fuzzy control with conventional PID control. Fuzzy reasoning rule of PID parameters is designed according to nonlinear and uncertainty of the hot embossing temperature control system. The performance of temperature control system was tested in the followed experiments. The stepped response tests show that the controller has satisfying dynamic and static performance. The temperature control precision can reach 0.2°C and temperature increasing/decreasing speed is greater than 1°C /s. It can satisfy the system requirements of the precise control of temperature in hot embossing device.