Abstract: The Penicillium expansum produces a toxic secondary metabolite, patulin. The PatC gene encodes the MFS transport protein, and transports the patulin precursor substance to the extracellular space, ultimately forming PAT. This has high reference value in the prevention of patulin. In order to study the transport mechanism of the PatC, the spatial structure of the PatC was predicted by using bioinformatics methods, and the interaction site and possible mechanism of E-ascladiol and the PatC were analyzed by molecular docking and molecular dynamics simulation. The results showed that the gene encoded 546 amino acids, containing 14 transmembrane helix and MFS functional domains. The molecular docking results showed that the protein had 4 binding sites with the E-ascladiol, namely SER353, TYR336, PRO339, and PRO188. Molecular dynamics simulations of 200 ns were performed for the Wild protein complex system and the P188A mutant system. The results showed that the small molecule substrate and the PatC were tightly bound, and that the protein's flexibility changed strongly after forming a complex in the Pro188~Ser197aa and Gly231~Val241aa regions. It could be inferred that these two regions might have functional sites. By analyzing the parameter data of the P188A mutant system, it could be predicted that PRO188 was an important target of the PatC protein, which could provide a basis for subsequent molecular experiments. The results of the research could lay the foundation for exploring the transport mechanism of patulin, and provide new strategies for the prevention of apple rot.