In open‐winding permanent magnet synchronous machine (OW‐PMSM) applied in electric vehicular system, two voltage sources composed of battery packs are applied. For safety and better performance, the over‐discharge on one of these two voltage sources should be avoided and their state of charges (SOCs) should be controlled in balance. On this basis, a reference voltage redistribution‐based control scheme is proposed to balance the SOCs of OW‐PMSM system in this letter, which utilizes the SOCs of the two voltage sources to distribute the reference voltages into two inverters. With the proposed method, the SOCs of the two voltage sources can be controlled in balance dynamically, while the synthesis of the reference voltage is not affected. The performance of the proposed method is validated experimentally.