The provisions of the new Food Safety Law on administrative penalty have changed from individual-oriented to legal person-oriented, the intensity of punishment has increased and the number of punished objects for the same illegal act has increased, which is the institutional motivation for many administrative penalty disputes that did not exist before. In the practice of administrative penalties for food safety, the increasing possibility of abusing discretion by administrative supervision departments, the lack of operational rules and standards for administrative penalties, and the lack of scientific and unified hearing procedures are the practical mechanisms that may lead to administrative penalty disputes. Therefore, in order to effectively curb and resolve administrative penalty disputes from the source, we can promote the improvement of the food legal system and the modernization of the governance capacity from the dimensions of establishing an open system of administrative penalty decision-making process, formulating rules for the implementation of administrative penalties for food safety and establishing a scientific and standardized hearing procedure for administrative penalties, so as to enhance the effectiveness of food safety supervision.