Since the three-phase photovoltaic system was susceptible to dead time effect, non-linear loads such as periodic disturbances would cause the output current waveform distortion. When three-level NPC inverter was working, the offset of neutral point voltage would reduce the output power quality of the system. To solve these problems, a complex control which combines the current PI closed loop control with repetitive control was proposed. The repetitive control based on internal model principle can effectively suppress periodic disturbances of the photovoltaic system. Meanwhile the nine-segment SVPWM divided a sample period into nine sections and increased the action time of small vector. The switch sequence was completely symmetrical and the same positive small vectors were adopted as first active vectors. And a closed-loop control system was proposed to control the neutral-point potential in real time, which was helpful to reducing harmonic content of the output current. Simulation results show that three-phase photovoltaic inverter based on composite repetitive control with using nine-segment SVPWM can not only balance the neutral-point potential but also make the output current have a better stability and less harmonic content. And the output current can have a good track to the grid voltage to achieve the same frequency and phase, which make the active power output at full load.