The symmetry of three-phase output voltages is very important in the evaluation of the performance of AC power supply. In order to obtain high quality output voltage waveforms of three-phase UPS (uninterruptible power supply) under unbalanced loads and nonlinear loads, this paper analyzed the mechanism of the asymmetry of output voltages of UPS, and proposed a multiplex control scheme combining repetitive control with PI control based on DSP under synchronous positive/negative reference frame coordination. Power switch transistors were applied to Space Vector Pulse Width Modulation (SVPWM) model. Negative sequence components of voltages have almost been eliminated, and zero sequence components and harmonics of voltages have been weakened effectively. The prototypes of 30-500 kVA UPS have been developed, and the experiment results have verified the validity of the proposed control scheme.