Objective To investigate and analyze the standardized management and clinical application of food for special medical purposes （FSMP） in secondary and above medical institutions of China.Methods In the form of online questionnaire， the medical institutions in 34 provinces / municipalities were sampled through the platforms of Sichuan Provincial Clinical Nutrition Quality Control Center and the Clinical Nutrition Discipline Alliance of West China Hospital.Results A total of 300 valid questionnaires were collected. In terms of FSMP management： 24.3% of medical institutions set up FSMP management committee； 64.3% of medical institutions formulated the catalogue of FSMP. Medical institutions with FSMP warehouses and FSMP preparation rooms accounted for 47.3% and 50.7%， respectively. 40.7% of medical institutions incorporated FSMP into information management； 43.3% of medical institutions charged unified coding fees. For clinical application of FSMP： 94% of medical institutions required nutrition risk screening before FSMP prescription； 84.7% of medical institutions required qualified prescribers； nearly 90% of medical institutions prescribed FSMP by nutritionists； 67.3% of medical institutions required the superior clinicians/ nutritionists to review the FSMP prescription before implementation. The adverse reaction of FSMP use was monitored in all 300 medical institutions， and only 30.7% reported the monitoring data of the adverse reactions to the provincial / municipal clinical nutrition quality control center.Conclusion The government should strengthen the construction of specialized fee catalogue and the unification of prescription qualification training； medical institutions at all levels， especially hospitals in the western region and secondary hospitals nationwide， should set up FSMP management committee as soon as possible， and integrate FSMP into the hospital information system. The clinical nutrition discipline should strengthen the formulation of clinical norms， detailed rules for the application of FSMP and supervision system. Safety monitoring and effectiveness evaluation should be strengthened so as to maximize the value of nutritional treatment of FSMP.