An electric energy harvesting circuit was designed for microbial fuel cells. Because of the account of the low output of the microbial fuel cell( about 0.5 mW), it was inadequate to drive the load or the boosted circuit. Therefore, this paper employed a charge pump to harvest the electric energy of the microbial fuel cell and stored it in a super-capacitor as the starting voltage. A super capacitor was taken as the energy storage component, then, the voltage was transferred to the needed value. An electronic switch was designed between the charge pump and the boost circuit, which could switch on and off automatically according to the setting threshold. Experimental results indicate that the circuit can operate at the input of 0.3 V, 0.5 mA. The electronic switch is closed at 2.2 V and opened at 1.6 V, and the charge-discharge in circulation is implemented automatically with a charge speed in direct proportion to the input voltage and indirect proportion to the energy storage capacitor. Furthermore, the final voltage is boosted to 3.3 V or 5 V, which can be changed on the basis of loads. In conclusion, the circuit satisfies the microbial fuel cell requirement of low power input. It can harvest the electrical energy generated from the sewage disposal, and can supply power for a water measurement system in outdoor with an intermittence.