Accurate prediction of the Remaining Useful Life (RUL) of lithium-ion batteries is essential for enhancing energy management and extending the lifespan of batteries across various industries. However, the raw capacity data of these batteries is often noisy and exhibits complex nonlinear degradation patterns, especially due to capacity regeneration phenomena during operation, making precise RUL prediction a significant challenge. Although various deep learning-based methods have been proposed, their performance relies heavily on the availability of large datasets, and satisfactory prediction accuracy is often achievable only with extensive training samples. To overcome this limitation, we propose a novel method that integrates sequence decomposition algorithms with an optimized neural network. Specifically, the Complementary Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN) algorithm is employed to decompose the raw capacity data, effectively mitigating the noise from capacity regeneration. Subsequently, Particle Swarm Optimization (PSO) is used to fine-tune the hyperparameters of the Bidirectional Gated Recurrent Unit (BiGRU) model. The final BiGRU-based prediction model was extensively tested on eight lithium-ion battery datasets from NASA and CALCE, demonstrating robust generalization capability, even with limited data. The experimental results indicate that the CEEMDAN-PSO-BiGRU model can reliably and accurately predict the RUL and capacity of lithium-ion batteries, providing a promising and reliable method for RUL prediction in practical applications.