The International Maritime Organization (IMO) is enforcing increasingly stringent regulations on ship carbon emissions, The International Maritime Organization (IMO) has been implementing progressively strict regulations on ship carbon emissions, leading to the adoption of the virtual arrival (VA) method by many vessels to reduce their carbon footprint. However, the effectiveness of the traditional VA method often varies in busy ports with complex traffic organization scenarios. To address this, our study presents a novel, comprehensive model that integrates vessel scheduling with the VA approach. This model is designed to achieve a dual objective: reducing carbon emissions through Virtual Arrival and simultaneously minimizing vessel waiting times. In addition to these goals, it incorporates essential aspects of safety, efficiency, and fairness in port management, utilizing the NSGA-2 algorithm to find optimal solutions. This model has been tested and validated through a case study at Ningbo-Zhoushan port, employing its dataset. The results demonstrate that our innovative model and algorithm significantly outperform traditional scheduling methods, such as First-Come-First-Serve (FCFS) and Virtual-Arrival Last-Serve (VALS), particularly in terms of operational efficiency and reduction in vessel carbon emissions.