Precise prediction of voltage degradation is critical for the prognostics and health management of proton exchange membrane fuel cells (PEMFCs). The performance degradation of PEMFCs is governed by a complex coupling of multiple physicochemical mechanisms, including catalyst layer and proton exchange membrane degradation. Crucially, these internal degradation processes evolve across highly heterogeneous time scales, ranging from transient high-frequency fluctuations to low-frequency and long-term irreversible performance fade. Conventional predictive models, which typically rely on single-scale architectures or fixed receptive fields, are inherently ill-equipped to simultaneously decouple and capture these cross-scale temporal dynamics. To tackle this challenge, this paper innovatively proposes a multi-scale deep learning framework that integrates a multi-scale degradation trend perception module, a long short-term memory (LSTM)-based encoder–decoder architecture, and a multi-head attention mechanism. One-dimensional convolutional layers with different kernel sizes are employed to simultaneously extract local temporal features at multiple granularities, followed by the LSTM encoder–decoder to model long-range temporal dependencies, while the cross-attention mechanism dynamically allocates attention across the encoded context at each autoregressive decoding step. Experimental outcomes indicate that the proposed model realizes excellent predictive accuracy across five evaluation indices in comparison with standard baselines. In particular, the mean absolute percentage error (MAPE) reaches 1.6696%, and the maximum absolute percentage error (Max-APE) is strictly bounded within 5%, substantiating the reliability of the proposed framework for high precision and long-horizon health prognostics for PEMFCs.