At present，the study of the internal restriction mechanism on discretion of administrative enforcement is relatively rare，which，to a certain extent，leads to the shortage in theory and practice in this field. With the methods of theoretical research and empirical study，and the results of comparisons of the legal provisions and field investigations，the article is to evaluate and analyze the existing problems and reasons on the discretion of administrative penalties currently in operation and standardize，and explore the internal restriction mechanism on discretion of food and drug administrative penalty in respect of the application rules and procedures.