Based on the average value model, the capacitor repetitive charging system of pulsed homopolar inductor alternator is studied. The variation law of sub-transient flux linkage during the charging process is analyzed, as well as the impact of sub-transient flux linkage variation on charging performance. Simulation and calculation results show that the sub-transient flux linkage gradually decrease during the charging process. When the charging time is equivalent to the electromagnetic time constant of the generator, the decrease in the sub-transient flux linkage during the charging process leads to a significant decrease in the charging voltage, so the impact of the sub-transient flux linkage change must be considered. The impact of excitation power supply with constant current control function on the regulation during charging is further studied, and it is pointed out that in order to reduce the insulation requirements of the generator, a gradual rise of the excitation current in the repetitive charging and discharging pulse mode should be adopted.