In order to facilitate the selection of an optimal topological structure for rational pulsed capacitor charging power supplies(CCPS), this paper presents a comparative analysis of CCPS based on permanent magnet excited(PME) and electrically excited(EE) homopolar inductor alternators(HIA). The findings indicate that the d-axis transient inductance of the PME HIA is marginally greater than that of the EE HIA, a result that contradicts initial expectations. Notably, the PME HIA does not require consideration of transient flux variations, whereas the EE HIA does. The study establishes relationships among the enhancement of charge performance, efficiency, capacitance, frequency, and field winding(FW) resistance. It is observed that as capacitance, frequency, and FW resistance increase, there is a corresponding improvement in charge performance. The equipotential line representing the enhancement of charge performance approximates an inverse proportional function, suggesting that if the product of FW resistance and capacitance, or the product of FW resistance and frequency, remains constant, the improvement in charge performance will also be constant. Furthermore, it is noted that as capacitance and frequency increase, the improvement in efficiency diminishes, which is contrary to the trend observed in charge performance. To comprehensively evaluate the enhancement of charge performance and efficiency, a weighted function is proposed. This function aids in the selection of a rational topological structure for CCPS, distinguishing between those based on PME HIA and those based on EE HIA. Based on the results derived from the weighted improvement analysis, appropriate topological structures for CCPS can be identified according to varying capacitance, frequency, and FW resistance. Specifically, when the product of capacitance and FW resistance, or the product of frequency and FW resistance, is substantial, the PME HIA is recommended; conversely, the EE HIA is preferred in other scenarios.