In recent years, due to the non-renewable nature of fossil resources and the global warming and environmental pollution caused by their use, the energy field has undergone great changes, and the proportion of new energy sources has been increasing, among which hydrogen energy has been hailed as the choice of the future. However, the environmental pollution problem in the production process of hydrogen energy supply chain enterprises has brought severe challenges to the sustainable development of supply chain raise funds. This paper selects two main supply chains of methanol and ammonia as the research objects, establishes the evaluation criteria of a green financing certificate and the evolutionary game model of methanol and ammonia supply chains for choosing to adopt a green supply chain strategy or traditional supply chain strategy, and simulates and analyzes the evolutionary game model to provide a reference for the sustainable development of supply chain financing.