The prefabricated building has been proven to be an effective approach for enhancing the sustainability of the construction industry. In recent years, the Chinese government has promulgated a series of policy documents to promote the advancement of prefabricated buildings. However, in practice, there are still numerous problems related to design, production, and construction, as well as the coordination between various stages. This study aimed to fill the gap in research regarding the application of EPC (Engineering–Procurement–Construction) in prefabricated buildings in China. As most of the risks of projects are borne by general contractors in the EPC mode, the risks faced by prefabricated building projects using EPC were systematically analyzed in this study from the perspective of general contractors. After learning about the risks of assembly construction in different countries, this study conducted a questionnaire survey to establish an evaluation system, and a comprehensive evaluation method was put forward to determine the weight of each indicator. Furthermore, an evaluation model based on grey–fuzzy theory was developed in this study, which was applied to a real project in Nanjing, China. The results indicated the applicability of the established evaluation system and model and determined the risk level of the project. Additionally, in this case study, it was found that construction and design were the major factors determining the risk level of the project. This study contributes to the body of knowledge regarding the integration of EPC in prefabricated buildings, which has practical application value for general contractors when conducting risk assessments.