In the context of global climate governance and the International Maritime Organization’s (IMO) stringent carbon reduction targets, the transition to green shipping fuels faces systemic challenges in supply chain coordination. This study focuses on the strategic interactions between governments and enterprises in the construction of green fuel supply chains. By constructing a multidimensional scenario framework encompassing time, technological development, social attention, policy intensity, and market competition, and using evolutionary game models and system dynamics simulations, we reveal the dynamic evolution mechanism of government–enterprise decision making. System dynamics simulations reveal that (1) short-term government intervention accelerates infrastructure development but risks subsidy inefficiency; (2) medium-term policy stability and market-driven mechanisms are critical for sustaining enterprise investments; and (3) high social awareness and mature technologies significantly reduce strategic uncertainty. This research advances the application of evolutionary game theory in sustainable supply chains and offers a decision support framework for balancing governmental roles and market forces in maritime decarbonization.