Abstract: Under China’s dual-carbon goals and the deep decarbonization of international shipping, selecting appropriate green fuel pathways has become a central issue for low-carbon maritime transition. This study adopts a well-to-wake perspective and examines 20 representative Chinese ports, developing an integrated framework that combines renewable energy modeling, fuel cost assessment, techno-economic analysis, and policy scenario simulation. Renewable hydrogen, ammonia, methanol, and conventional fuel oil are systematically compared across nearshore and deep-sea scenarios. Results show significant spatial variation in renewable fuel costs, primarily driven by electricity prices. Hydrogen and ammonia offer superior emission reduction potential but are constrained by current economic feasibility. With carbon regulations such as the EU ETS, the competitiveness of green fuels improves significantly. Methanol dominates in deep-sea scenarios, while hydrogen and methanol are competitive in nearshore contexts, and ammonia shows strong long-term potential. A phased and differentiated transition pathway is proposed accordingly.