Battery management system (BMS) in autonomous underwater vehicle (AUV) not only can measure the main parameters of battery packs such as current, voltage, and temperature, but also estimate the state of charge (SOC) of battery packs. This paper proposes a broad approach for the design of battery management system. The new design can improve the cycle life and safety capability. With the model well designed, the parameters required are obtained and the SOC estimation is completed. Extended Kalman filter (EKF) was chosen to make the last estimate with the reliable battery model which was used to the non-linear system to estimate SOC and suitable for AUV applications. The experiments results prove that the data measured by battery management system have high precision and reliability. The estimated error of SOC was also small, which was better than other approaches for estimate.