<p>Green logistics has become an important pathway for promoting sustainable port development under the dual pressures of carbon reduction and maritime economic transformation. However, existing studies mainly focus on mature ports in developed coastal regions, while research on emerging ports remains limited. In addition, traditional efficiency evaluations often neglect undesirable outputs and the dynamic evolution of productivity. To address these gaps, this study evaluates the green logistics efficiency of the Beibu Gulf Port (Qinzhou, Fangchenggang, and Beihai) during 2014–2023 using a Super-SBM–GML model that incorporates undesirable outputs and dynamic productivity analysis. The results show that the overall green logistics efficiency of the Beibu Gulf Port exhibits a gradual upward trend, although the efficiency level remains below the optimal frontier. Significant spatial heterogeneity exists among the three ports, with Qinzhou Port demonstrating the highest static efficiency, while Fangchenggang Port shows relatively stronger dynamic productivity growth. Furthermore, improvements in green total factor productivity are mainly driven by efficiency catch-up effects rather than substantial technological progress, indicating that green technological innovation remains a key constraint on sustainable port transformation. This study extends green logistics efficiency research from mature ports to emerging port clusters within the context of the Belt and Road Initiative (BRI) and the New International Land–Sea Trade Corridor (ILSTC). The study further proposes an “Anchor–Corridor–Network” framework to explain how technological upgrading, institutional coordination, and regional integration jointly drive the green transition of emerging ports. The findings provide practical implications for promoting low-carbon port transformation, regional logistics integration, and sustainable maritime governance in developing economies.</p>