Evaluating the quality risk level in the food supply chain can reduce quality information asymmetry and food quality incidents and promote nationally integrated regulations for food quality. In order to evaluate it, a quality risk evaluation indicator system for the food supply chain is constructed based on an extensive literature review in this paper. Furthermore, a mathematical model based on the fuzzy comprehensive evaluation model (FCEM) and failure mode, effects, and criticality analysis (FMECA) for evaluating the quality risk level in the food supply chain is developed. A computational experiment aimed at verifying the effectiveness and feasibility of this proposed model is conducted on the basis of a questionnaire survey. The results suggest that this model can be used as a general guideline to assess the quality risk level in the food supply chain and achieve the most important objective of providing a reference for the public and private sectors when making decisions on food quality management.