This paper studies the state of charge (SOC) estimation of supercapacitors and lithium batteries in the hybrid energy storage system of electric vehicles. According to the energy storage principle of the electric vehicle composite energy storage system, the circuit models of supercapacitors and lithium batteries were established, respectively, and the model parameters were identified online using the recursive least square (RLS) method and Kalman filtering (KF) algorithm. Then, the online estimation of SOC was completed based on the Kalman filtering algorithm and unscented Kalman filtering algorithm. Finally, the experimental platform for SOC estimation was built and Matlab was used for calculation and analysis. The experimental results showed that the SOC estimation results reached a high accuracy, and the variation range of estimation error was [−0.94%, 0.34%]. For lithium batteries, the recursive least square method is combined with the 2RC model to obtain the optimal result, and the estimation error is within the range of [−1.16%, 0.85%] in the case of comprehensive weighing accuracy and calculation amount. Moreover, the system has excellent robustness and high reliability.