Zhejiang (China) has several large ports and is an early province in implementing port integration policy. This study evaluates the green efficiency of major ports in Zhejiang (China) for 2019–2022 using the Super-slack-based measure (Super-SBM) model with CO2 emissions. This study provides theoretical and empirical analyses of the effect of integration policy on port green efficiency. The results show that Ningbo and Zhoushan ports have high green efficiency. However, the green efficiency of Taizhou, Jiaxing Inland and Wenzhou Ports needs to be improved urgently because of the massive investment in coastline and berths and high carbon emissions. The port green efficiency can be improved by implementing an integration policy between ports geographically close, such as Ningbo, Zhoushan and Jiaxing ports. Higher port city levels and fixed asset investment positively impact port green efficiency. The findings provide a reference for policymakers to improve the green efficiency of ports.