State-of-charge (SoC) estimation is one of the core functions of battery energy management systems. An accurate SoC estimation can guarantee the safe and reliable operation of the batteries system. In order to overcome the practical problems of low accuracy, noise uncertainty, poor robustness, and adaptability in parameter identification and SoC estimation of lithium-ion batteries, this paper proposes a joint estimation method based on the adaptive extended Kalman filter (AEKF) algorithm and the adaptive unscented Kalman filter (AUKF) algorithm in multiple time scales for 18,650 ternary lithium-ion batteries. Based on the slowly varying characteristics of lithium-ion batteries’ parameters and the quickly varying characteristics of the SoC parameter, firstly, the AEKF algorithm was used to online identify the parameters of the model of batteries with a macroscopic time scale. Secondly, the identified parameters were applied to the AUKF algorithm for SoC estimation of lithium-ion batteries with a microscopic time scale. Finally, the comparative simulation experiments were implemented, and the experimental results show the proposed joint algorithm has higher accuracy, adaptivity, robustness, and self-correction capability compared with the conventional algorithm.