Accurate estimation of lithium-ion battery (LIB) state of health (SOH) is critical for prolonging battery life and ensuring safe operation. To address the limitations of existing data-driven models in robustness and feature coupling, this paper presents a new Bagging-PiFormer framework for SOH estimation. The framework integrates ensemble learning with an improved Transformer architecture to achieve accurate and stable performance across various degradation conditions. Specifically, multiple PiFormer base models are trained independently under the Bagging strategy to enhance generalization. Each PiFormer consists of a stack of PiFormer layers, which combines a cross-channel attention mechanism to model voltage–current interactions and a local convolutional feed-forward network (LocalConvFFN) to extract local degradation patterns from charging curves. Residual connections and layer normalization stabilize gradient propagation in deep layers, while a purely linear output head enables precise regression of the continuous SOH values. Experimental results on three datasets demonstrate that the proposed method achieves the lowest MAE, RMSE, and MAXE values among all compared models, reducing overall error by 10–33% relative to mainstream deep-learning methods such as Transformer, CNN-LSTM, and GCN-BiLSTM. These results confirm that the Bagging-PiFormer framework significantly improves both the accuracy and robustness of battery SOH estimation.