State of health (SOH) estimation plays a vital role in ensuring the safe and stable operation of lithium-ion battery management systems (BMSs). Data-driven methods are widely used to estimate SOH; however, existing methods often suffer from fixed or excessively high feature dimensions, impacting the model’s adjustability and applicability. This study first proposed a layered knee point strategy based on the charging voltage curve, which reduced the complexity of feature extraction. Then, a new hybrid framework called the adaptive gated sequence network (AGSN) model was proposed. This model integrated independently recurrent neural network (IndRNN) layers, active state tracking long short-term memory (AST-LSTM) layers, and adaptive gating mechanism (AGM) layers. By integrating a multi-layered structure and an adaptive gating mechanism, the SOH prediction performance was significantly improved. Finally, batteries under different operating conditions were tested using the NASA battery dataset. The results show that the AGSN model demonstrated higher accuracy and robustness in battery SOH estimation, with estimation errors consistently within 1%.