The present invention discloses a three electric level inverter control system. It contains three electric level voltage source inverter (NPC), field programmable gate array (FPGA), digital signal processor (DSP), wherein FPGA field programmable gate array (FPGA) receiving digital signal processor (DSP) sent control voltage instruction generating three electric level voltage source inverter (NPC) control signal. The present invention also discloses three level inverter control method, featuring 1, digital signal processor (DSP) transmitting space voltage vector amplitude value m and argument for controlling three level inverter triphase reference voltage, 2, field programmable gate array (FPGA) receiving DSP sent space voltage vector amplitude value m and argument, generating signal Vca, Vcb, Vcc, through direct current biasing and dead zone compensation techniques processing to generate three-phase voltage modulation signal Vca **, Vcb **, Vcc **, 3, finally respectively comparing with positive triangular wave, negative triangular wave to generate control pulse. The present invention overcomes the insufficiency of current pulse width modulation method (SVPWM) and special harmonic cancellation method (SHE-PWM), provides a fine rapidity, simple controlling, and practical three level inverter control system and method.