To enhance voltage prediction accuracy in energy storage batteries and address the limitations of fixed threshold warning methods, a fault warning approach based on an improved Autoformer model and adaptive thresholds is proposed. First, a spatiotemporal filtering layer is introduced into the autocorrelation mechanism to analyze the trend features of voltage sequences across different frequency domains. Additionally, an adaptive gating residual connection is used to link the sublayer and current layer output features, which helps to improve the model's adaptive feature selection capability. This innovation enables the development of a robust voltage prediction model based on the enhanced Autoformer. Then, a similarity‐based adaptive threshold, using interval estimation, is employed to rapidly track variations in battery voltage, enabling dynamic adjustment of voltage thresholds. Finally, the proposed method is validated with real voltage data from an operational energy storage station. The experimental results shows that the proposed model has higher accuracy and robustness compared to similar methods. The adaptive threshold can reduce the false alarm rate by ≈18% and issue alarms at three sampling points ahead of the battery management system alarm, improving fault warning accuracy and illustrating that early fault warning is effectively and practically carried out using the method.