This paper introduces a hybrid framework for port container throughput forecasting, which is essential in global trade and transportation systems. It uses a multidisciplinary method that combines artificial intelligence, link prediction, and complex networks. To better grasp the interconnection and dynamics of port operations, time series data are first transformed using complex network theory into a network structure. The framework applies 13 similarity metrics, encompassing various aspects of network structural similarity, to form a feature set representing the complex port operation network. The most effective features are selected using the maximum relevance minimum redundancy (mRMR) method, adhering to systems theory’s efficiency principles. These features are processed through SVM, DNN, and LSTM models for link prediction, which is crucial for forecasting in port logistics. Finally, the methodology concludes with regression analysis to obtain container throughput forecasts, which is a key metric in port systems management. Case studies of Shanghai Port and Shenzhen Port validate the framework’s effectiveness, demonstrating a significant improvement in forecasting accuracy over the baseline models. This study contributes to systems analysis by showcasing a hybrid, AI-enhanced approach for managing and forecasting critical aspects of maritime trade systems.