<p>The rapid expansion of the port industry has led to significant environmental challenges, particularly pollution from shipping activities, which emit carbon dioxide and contribute to issues such as ocean acidification. Despite growing attention from scholars and governments, the evaluation of port productivity often neglects a green perspective. To address this gap, this study introduces a justified and structured green total factor productivity (GTFP) assessment framework and demonstrates the impact of biased technological changes in port operations. Focusing on the operational processes of port companies, we divide their activities into two sub-processes: production operation and value transformation. Using a two-stage Russell-based directional distance function (RDDF) model, we evaluate the GTFP of 13 Chinese port listed companies from 2012 to 2021. The results reveal that the overall GTFP of Chinese port listed companies exhibits an upward trend, driven more by technological changes than efficiency improvements. In the production operation sub-process, input-biased technological changes play a significant role, with labor, physical inputs, and costs prioritized in that order. Notably, labor emerges as a critical factor in promoting green technological progress in China. In the value transformation sub-process, output-biased technological changes have a greater impact on technological changes, with the elements of output-biased technological changes being desired outputs. This research not only enhance the accuracy of measurement but also support national low-carbon development goals, providing new strategies for policymakers and port operators to balance economic growth with environmental sustainability, highlighting the importance of aligning industrial development with environmental policies.</p>