The idea of electric-drive-reconstructed onboard charger (EDROC) systems, along with the concept of dual-channel charging, offers a novel design, thought to enhance the integration and fault tolerance of the charging system of electric vehicles (EVs). This article investigates a dual-channel EDROC incorporating an asymmetrical six-phase permanent magnet synchronous machine (ASPMSM). A unique operation mode, called the unbalanced charging voltage operation mode, exists in this topology, in case the voltages of the two batteries are unequal. This unbalance results in different winding currents following through two channels, leading to an undesired charging torque in the machine. To ensure the safety of the system, an effective charging torque elimination method, based on dual-channel winding current balance, is proposed, which achieves a dot-shaped current path of torque generation-associated subspace (i.e., α–β subspace) by balancing the dual-channel charging power. Eventually, a controller is designed for the system and a prototype is created, to validate the effectiveness of the proposed method.