The control strategy of electric vehicles mainly depends on the power battery state-of-charge estimation. One of the most important issues is the power lithium-ion battery state-of-charge (SOC) estimation. Compare with the extended Kalman filter algorithm, this paper proposed a novel adaptive square root extended Kalman filter together with the Thevenin equivalent circuit model which can solve the problem of filtering divergence caused by computer rounding errors. It uses Sage-Husa adaptive filter to update the noise variable, and performs square root decomposition on the covariance matrix to ensure its non-negative definiteness. Moreover, a multi-scale dual Kalman filter algorithm is used for joint estimation of SOC and capacity; the forgetting factor recursive least-square method is used for parameter identification. To verify the feasibility of the algorithm under complicated operating conditions, different types of dynamic working conditions are performed on the ternary lithium-ion battery. The proposed algorithm has robust and accurate SOC estimation results and can eliminate computer rounding errors to improve adaptability compared to the conventional extended Kalman filter algorithm.