Three-level NPC inverters have been put into practical use for years especially in high voltage high power grids. This paper researches three-level active power filters (APFs). In this paper a mathematical model in the d-q coordinates is presented for 3-phase 3-wire NPC APFs. The deadbeat control scheme is obtained by using state equations. Canceling the delay of one sampling period and providing the predictive value of the harmonic current is a key problem of the deadbeat control. Based on this deadbeat control, the predictive output current value is obtained by the state observer. The delay of one sampling period is remedied in this digital control system by the state observer. The predictive harmonic command current value is obtained by the repetitive predictor synchronously. The repetitive predictor can achieve a better prediction of the harmonic current with the same sampling frequency, thus improving the overall performance of the system. The experiment results indicate that the steady-state accuracy and the dynamic response are both satisfying when the proposed control scheme is implemented.