In the three phase inverters power supply system, asymmetry of the output voltage may lead to local overload of the inverter and impair the reliability of the power supply system. To maintain symmetric three phase output voltage is one of the most important duties of the inverter, and asymmetry of the output voltage is mainly caused by unbalanced loads in the power supply system. To solve this problem, the mechanism of asymmetric output voltage of the three phase inverter under unbalanced loads is analyzed based on symmetrical component decomposing and the superimpose theory. Analysis show that positive-sequence, negative-sequence and zero-sequence components of the output voltage have different effect on the performance of compensation, and a simple and feasible synchronous positive-sequence negative-sequence reference system controller is proposed which can effectively compensate the output voltage distortion of the three phase inverter under the unbalanced loads, thus, symmetric output voltages of the three phase inverter under unbalanced load can be ensured. Matlab simulation is performed to verify the theoretical analysis results of the proposed control method