Objective To construct an index system for the rational use of foods for special medical purposes (FSMP) by medical institutions. Methods Based on the literature review and the survey of 300 medical institutions, we developed a questionnaire for expert consultation and conducted two rounds of expert consultation using Delphi method and consensus meeting method to determine the final index system for the rational use of FSMP in medical institutions. Results After two rounds of expert consultation and expert consensus conference meetings, it was finally determined that medical institutions should reasonably use the FSMP comprehensive evaluation index system, including 3 first-level catalog indicators, 17 second-level catalog indicators, and 13 third-level catalog indicators. Conclusion This index system can help promote the rationalization and standardization of FSMP clinical application in medical institutions in China and improve the quality of clinical nutrition care.