In order to study the hot pressing bonding process of cycloalkene copolymer（COC）microfluidic chip, a temperature control system based on STM32 MCU was designed. The system was equipped with FreeRTOS multitask operating system, thermistor NTC was used as temperature sensor, Butterworth low-pass filter was used for temperature data process, fuzzy incremental PID control algorithm was used, and pulse width modulation PWM was used for temperature control of semiconductor refrigeration chip, then accurate temperature control in bonding process temperature of 75~85 ℃ was realized. The overshoot of the system is less than 1%, the heating rate is above 0.50 ℃/s, and the cooling rate is above 0.34 ℃/s. The temperature control accuracy reaches ±0.3 ℃.