As an important part of the comprehensive transportation system, ports play an important role in economic development. In the context of the ‘3060 double carbon’ target, the high-quality development (HQD) of ports is receiving attention from many parties. The aim of this paper is to examine the dynamic evolution of HQD in China’s coastal ports from the perspective of green total factor productivity (GTFP). Firstly, the calculation standards of undesirable outputs are given, and integrated environmental dumping indicator is calculated by the combination weight calculation model based on game theory. Then, the super-efficiency DEA-GML (Data Envelopment Analysis-Data Envelopment Analysis-Global Malmquist-Luenberger) index model based on directional distance function (DDF) is used to measure the GTFP growth of ports. Furthermore, the dynamic evolution of GTFP growth of ports is explored using the kernel density estimation. The findings show that the GTFP growth of coastal ports has continued to improve during the examined period. However, there is the problem that port construction inputs cannot bring effective outputs, and there is a bifurcation that tends to stabilize within coastal ports. Finally, targeted policy implications are given to promote HQD of ports.