In traditional battery equalization strategy, open-circuit voltage (OCV) of battery cells was used to judge the difference of SOC between them. However, OCV is not only determined by SOC but also influenced by internal resistance, polarization voltage, capacity, and other nonlinear factors. As a result, OCV is not an ideal indicator of SOC differences, especially in transient conditions. In order to control battery consistency accurately, it is best to use SOC directly as standard for battery consistency judgment and control. To achieve this, an algorithm that can estimate SOC of multiple battery cells simultaneously with low computational complexity and high accuracy is needed. Limited by computing speed of Battery Control Unit (BCU), existing SOC estimation method is hard to estimate SOC of each battery cell simultaneously with high accuracy. In this research, a new SOC estimation strategy was proposed to estimate SOC of multiple battery cells simultaneously for battery equalization control. Battery model is established based on experimental data, and a processor-in-the-loop test system was established to verify the actual performance of the proposed algorithm. Results of simulation and test indicate that the proposed algorithm can estimate SOC of multiple battery cells simultaneously and achieved good real-time performance and high accuracy.