Accurate estimation of the state of charge is crucial for the safe and reliable operation of the reconfigurable lithium battery energy storage system, and this paper proposes a method that can correct the initial error and accurately estimate the state of charge. Firstly, a new reconfigurable battery network based on a switching bypass type is proposed and the idea of estimating the state of charge for each battery module in this network is described. Secondly, the battery equivalent model with a dual resistor-capacitor parallel network is selected, and a set of lithium battery sample data is chosen for parameter identification. Then, the nonlinear state-space equations of the battery system are established according to the battery equivalent model, and the relationship curves between the open circuit voltage and the state of charge of the battery are fitted. The accurate estimation of the state of charge is estimated by the extended Kalman filter (Extended Kalman filter). Finally, a simulation model is built in the Matlab/Simulink environment, and the simulation results of the state of charge estimation method and the open circuit voltage method under constant current discharge and intermittent discharge conditions are compared. The results show that the estimation method can effectively correct the initial error and accurately estimate the state of charge of the battery, and the estimation accuracy of the method is better than the open circuit voltage method.