Under the context of China’s green agricultural transformation, the risk assessment of agricultural supply chain financing must balance economic benefits and environmental sustainability. However, existing studies often overlook the evaluation of overall supply chain risks and the long-term needs of sustainable agricultural development. To address this gap, this paper constructs a financial risk assessment index system for green agricultural supply chains. Building upon the traditional TOPSIS method, we integrate intuitionistic fuzzy set theory, entropy weight method, and expert scoring to develop a risk assessment approach that combines fuzzy information with objective weighting. This method reduces uncertainties in the evaluation process and establishes a comprehensive framework. Empirical validation using real-world data from agricultural enterprises further confirms the feasibility and practicality of the model.