For safe and efficient operation of electric vehicles (EVs), battery management system is essential. Nevertheless, a challenge lying in battery management systems is how to obtain an algorithm for state of charge (SOC) estimation that has both high accuracy and low computational cost. For this purpose, the battery parameters and SOC joint estimation algorithm based on bias compensation least squares and alternate (BCLS-ALT) algorithm are proposed in this paper. The battery model parameters are identified online using the bias compensation least squares (BCLS), while the SOC is estimated applying the alternate (ALT) algorithm, which can switch the computational logic between H-infinity filter (HIF) and ampere-hour integral (AHI) to improve the computational efficiency and accuracy. The experimental results show that the accuracy of the SOC estimated by the BCLS-ALT algorithm is the highest, and the computational efficiency is also high, with the switching threshold SOCALT being set to 25%. Despite the 20% initial error and the 10% current drift, the proposed BCLS-ALT algorithm can obtain high accuracy and robustness of SOC estimation under different ambient temperatures and dynamic load profiles.