The mechanism of acceleration, loss, and wave–particle interaction of energetic particles in the magnetosphere is a research content of the Space Plasma Environment Research Facility, which is being built as a user facility at the Harbin Institute of Technology in China. Two magnetic perturbation coils are used to simulate the magnetic storm distortion and excite Alfvén wave perturbation. A capacitor-based pulsed power supply (PPS) system with a modular design is developed to excite the magnetic perturbation coils to generate the required amplitude and duration of the magnetic field. The two magnetic perturbation coils are the CRDI coil and CRDII coil and are excited by one set of PPSs. The PPS for the CRDI coil consists of two modules and can provide a pulsed current of no less than 132 kA at 0.12 ms when the charging voltage is 20 kV, and the duration of the pulsed current from the peak to 10% of the peak is no more than 0.7 ms. The PPS for the CRDII coil consists of five modules and can provide a pulsed current of no less than 16 kA at 0.45, 0.65, 0.8, 0.95, and 1.1 ms, and the duration of the pulsed current from the peak to 10% of the peak is no more than 4.5 ms. The detailed design of the PPSs has been discussed in this paper, and the discharge test of the PPSs is carried out to verify the design of the PPSs.