The sudden interruption of train power supply in an extreme environment will seriously threaten the safety of passengers and affect the operational efficiency of the railway system. In this case, the focus of attention becomes a method of running the train to the nearest rescue point based on the limited capacity of the on-board emergency energy storage device. Therefore, this paper reports research on the state of charge (SOC) estimation of train energy storage equipment to optimize the emergency traction strategy and energy utilization rate of trains to the maximum extent. First, with the emergency power supply of on-board lithium titanate batteries, the energy flow model of train emergency power supply is constructed for the first time. Second, based on the second-order equivalent circuit model and considering the utilization of regenerative braking energy, the relationship between battery capacity and open circuit voltage (OCV), temperature, current and SOC are constructed through experimental data, which significantly improves the accuracy and robustness of SOC estimation in complex and variable environments. Then, to effectively eliminate the impact of environmental on the estimation especially in the case of extremely low temperature (−20 °C), online model parameter discrimination and SOC estimation of lithium batteries are realized by combining recursive least squares with an optimal forgetting factor (FRLS) algorithm and a new temperature forgetting factor based adaptive extended Kalman filter (TFFAEKF) algorithm. The experimental results show that the proposed method achieves accurate SOC estimation, and the maximum error is less than 1% at different temperatures.