<p>Pursuing high-average-power free electron lasers (FEL) imposes increasingly stringent requirements on electron sources. An electron gun equipped with a photocathode is crucial for generating high-quality, high-current electron beams, which requires a high-voltage direct current power supply (HVDCPS) rated at several hundred kilovolts, with stability superior to 10^–5 to maintain a stable electric field. A three-phase input-parallel output-series (IPOS) LCC resonant converter is a suitable topology for this application. However, voltage imbalance arising from component parameter tolerances can result in up to a twofold difference between the highest and lowest phase voltages, posing a significant challenge to power supply stability. This study proposes a voltage balancing method based on negative sequence component injection. Combining the three-phase output voltages enables a new set of control phasor <i>X</i> to equalize output voltages across submodules. Opposing components are injected into the three-phase input voltage phasor based on the proportion of negative sequence components in <i>X</i>. This approach ultimately balances the output voltage by retaining only the positive sequence components of <i>X</i>. The effectiveness of the proposed method is experimentally validated. Results show that the voltage imbalance of the prototype decreases from 28.9% to 0.5% under full-load conditions after applying the balancing strategy. This method is also applicable to control systems with zero-sum three-phase phasors and can be extended to current balancing in the resonant tank.</p>