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The digital method of natural sampling sinusoidal pulse width modulation (SPWM) is studied based on the characteristics of neutral point clamped three-level inverters of Photovoltaic power generation system. Based on field programmable gate array (FPGA), A three-level natural sampling SPWM digital framework is constructed. The digital implementation methods of triangular carrier generation, sinusoidal modulation waveform generation, switching state combination configuration and dead-zone setting are studied. A ultra-realtime comparison calculation method of switching time based on FPGA technology is proposed in this paper. This method avoids complex calculation such as Taylor series expansion and convergence judgment in natural sampling SPWM. Under the same conditions, the harmonic content of the SPWM output waveform using this method is smaller than that of the symmetrical regular sampling method. And the harmonic content is equivalent to that of natural sampling. The digital natural sampling method can further improve the quality of output waveform and the stability of DC bus voltage of three-level inverters. The theoretical research is realized by VHDL (Very High Speed Integrated Circuit Hardware Description Language) and FPGA chip. The experimental results prove the correctness and feasibility of the digital method.