The performance of the neutral beam injection arc power supply seriously affects the stability of the arc discharge and the efficiency of the neutral beam heating. HL-2A device arc power supply adopts linear power supply technology based on thyristor phase-controlled voltage regulation and 12-pulse uncontrolled rectification; HL-2M test beam line device arc power supply adopts switching power supply technology based on super capacitor and IGBT full-controlled rectification. To optimize the performance of the power system, improve the arc discharge stability, the influence of sampling frequency on the stability of arc discharge is studied. By modeling the HL-2A and HL-2M power supply control systems, MATLAB is used to simulate the step response performance of the HL-2M arc current power supply control system and the HL-2A control system performance under different sampling frequencies, and analyze the impact of the sampling frequency on the system performance. Then, the ion source test platform is used to conduct arc discharge experiments at different sampling frequencies to verify the simulation results, and the experimental results are consistent with the simulation results. It is verified by experiments that the sampling frequency has great influence on the stability of arc discharge, while in the frequency adjustable range, increasing the sampling frequency can improve the performance of the control system and optimize the stability of arc discharge; the reason for the unstable arc discharge of HL-2A is the conduction characteristics of the thyristor and the filter circuit.