The high voltage power supply is an important part of the neutral beam injection heating system. It determines the beam energy and the quality of the extraction beam current. To meet the power demand of the neutral beam injection system of the HL-3 device, a modular high voltage power supply system based on pulse step modulation technology is designed, and it can achieve the rated voltage output by connecting power modules in series. Each power module uses a single-phase bridge rectifier and half-bridge output control, and a soft start circuit and an energy discharge circuit are designed so that the power supply module can carry out function tests under the condition of utility power supply. The regulator module circuit is developed to realize the precise control of power supply output voltage by controlling the output voltage level of the regulator module. The power supply module and system are simulated using the Simulink toolbox in MATLAB, and tests of the soft start function, rated output and short circuit protection performance of the power supply are carried out. By building a 1600 V/50 A/5 s test prototype and a 80 kV/50 A/5 s test platform, the electrical performance of the power system module hasbeen experimentally verified. The simulation and experimental results show that the power module test prototype meets the rated output requirements and can stably realize 80 kV voltage output through series connection. The short circuit protection time is less than 6 μs, which can realize fast protection shutdown of the power supply and meet the performance requirements of the HL-3 device 5 MW neutral beam injection system for the high voltage power supply.