To advance energy conservation and emissions reduction in urban logistics systems, this study focuses on the green vehicle routing problems with time windows (GVRPTWs), which remains underexplored in balancing environmental and service quality objectives. We propose a comprehensive multi-objective optimization framework that addresses this gap by simultaneously minimizing total distribution costs and carbon emissions while maximizing customer satisfaction, quantified based on the vehicle’s arrival time at the customer location. The rationale for adopting this tri-objective formulation lies in its ability to reflect real-world trade-offs between economic efficiency, environmental performance, and service level, which are often considered in isolation in previous studies. To tackle this complex problem, we develop an improved Non-Dominated Sorting Genetic Algorithm III (NSGA-III) that incorporates three key enhancements: (1) an integer-encoded initialization method to enhance solution feasibility, (2) a refined selection strategy utilizing crowding distance to maintain population diversity, and (3) an embedded 2-opt local search operator to prevent premature convergence and avoid local optima. Comprehensive validation experiments using Solomon’s benchmark instances and a real-world case demonstrate that the presented algorithm consistently outperforms several state-of-the-art multi-objective optimization methods across key performance metrics. These results highlight the effectiveness and practical relevance of our approach in advancing energy-efficient, low-emission, and customer-centric urban logistics systems.