Traditional linear models struggle to capture the intricate relationship between dynamic container throughput and its complex interplay with economic fluctuations. This study introduces a novel, deep learning-based multivariate framework for precision in demanding landscapes. The framework consistently outperforms eight established benchmark models by employing vital economic indicators like GDP and port tonnage, identified through rigorous predictor importance analysis of an initial set of four variables, including imports and exports. Statistical significance is demonstrably achieved through the Diebold–Mariano and Wilcoxon rank-sum tests. Utilizing the Port of Singapore as a case study, the framework offers agile adaptability for the ever-evolving global supply chain. Comprehensive analyses ensure robustness, decoding intricate throughput dynamics. Incorporating noise-assisted multivariate empirical mode decomposition (NA-MEMD) for nonlinear decomposition and bidirectional long short-term memory (BiLSTM) for time series dependencies, this innovative approach holds promise for revolutionizing container throughput forecasting and enhancing competitiveness in the global market through optimized resource allocation and streamlined operations.