Peak Carbon and Carbon Emission Reduction has been a hot issue in the shipping industry for a long time, but it still faces serious challenges. One of the reasons for this is that there is still a lack of scientific guidance on carbon reduction in ports. Improving Port Carbon Emissions Efficiency (PCEE) is an effective means to achieve carbon neutrality. This study analyses the Carbon Emissions Efficiency (CEE) of ports in the Pearl River Delta (PRD) region, which can provide theoretical support for the development and optimization of green, efficient, and sustainable development strategies for ports. A Super efficiency Slack Based Measure model (Super-SBM) considering non-desired outputs was constructed to assess the static efficiency of carbon emissions and the potential for improvement of the ports using panel data of nine ports in the P PRD for the period 2010–2022; a Global Malmquist- Luenberger (GML) index to study the dynamic changes of port carbon emission efficiency. A comprehensive static-dynamic measurement of port carbon emission efficiency is carried out, and strategies for improvement are proposed. The results of the study show that: (1) there are obvious differences in efficiency among ports, and the mean value of PCEE of Shenzhen, Foshan, Zhongshan and Zhaoqing ports is greater than or equal to 1 during the study period; (2) during the study period, the mean value of the GML index is 1.03623, and the PCEE shows an increase, and ports have shown obvious improvement in green and low-carbon efficiency. (3) In the third category of ports with a low level of carbon emission efficiency and slow growth, improving resource allocation is an important method to improve PCEE.