<p>Sustainable development in container terminals (CTs) has become increasingly critical amid rising global trade volumes and environmental concerns. In this study, a novel hybrid framework is developed that integrates a hierarchical data envelopment analysis (HDEA) with quality function deployment (QFD) in order to evaluate and prioritize sustainable operational practices across multiple ports. Unlike existing approaches that emphasize costly technological interventions, our model focuses on cost-effective, implementable solutions such as truck appointment systems, yard truck pooling, and dual cycling strategies. Using empirical data from Taiwan’s three major container ports, in this study, hierarchical performance indicators are constructed encompassing air pollution, noise pollution, and traffic flow. The integration of QFD with HDEA ensures objective weight assignment and consistent benchmarking across ports. The results identify traffic flow management as the most pressing concern, with shipside and gate operations playing pivotal roles in improving sustainability performance. This study demonstrates the potential for combining engineering-based customer satisfaction modeling (QFD) with performance optimization methods (HDEA) in order to enhance the planning and measurement of sustainable development in terms of port logistics. This integrated framework contributes both theoretically and practically by providing a replicable model for evaluating sustainability initiatives in multi-node logistics systems. The findings offer actionable insights for policymakers, terminal operators, and researchers seeking to balance environmental responsibility with operational efficiency.</p>