In this paper a dsPIC microcontroller based temperature control system is developed for polymerase chain reaction (PCR) on-chip. PCR is one of the most important techniques in molecular biology and temperature control is the key technique of PCR. Yet, most of the works are based on PC, through an RS 232 interface to set and control the temperature. Here we design a temperature control system based on DSPIC Microcontroller. It can be much portable and cheaper than PC based systems. The system configuration mainly consists of a high precision, stable performance sensor PT1000, a signal amplification circuit, a PID algorithm. And then, we use MAX1978 to improve the accuracy of temperature control. After that we choose thermoelectric cooler (TEC) modules as actuator to improve system heating and cooling rate. It is believe that the portable PCR temperature control system will play an important role in the development of the Microfluidic PCR.