In half-bridge converter series Y-connection microgrid (HCSY-MG) systems, environmental factors such as wind speed and solar irradiance cause significant variations in the output power of individual wind and solar micro-sources. This results in imbalanced three-phase output power, leading to asymmetry in grid-connected currents, which can severely affect the system’s grid-connected operation. To address this issue, a control method combining positive-sequence component synthesized zero-sequence voltage injection with overmodulation compensation is proposed. This method synthesizes the zero-sequence voltage using a positive-sequence component that are in phase with the three-phase grid voltage, simplifying the calculation process compared to traditional methods. However, the power balancing capability of zero-sequence voltage injection is limited, and the system is prone to overmodulation when the degree of three-phase power imbalance is large. To mitigate this, overmodulation compensation is introduced by modifying the zero-sequence voltage, thereby expanding the system’s inter-phase power balancing range. This ensures that the system can continue to operate normally under significant inter-phase power imbalance and that the grid-connected currents meet grid code requirements. Finally, simulations and experiments verify the correctness and feasibility of the proposed control strategy.