Abstract: To analyze the inhibitory mechanism of Sanxiapeptin on the main postharvest spoilage fungus P. digitatum of citrus fruits, the morphology responded to Sanxiapeptin was observed by microscopy. The cell wall protective agent sorbitol and cell membrane protective agent ergosterol were used to analyze the inhibitory effects of Sanxiapeptin on the fungi. Through BGISEQ-500 research platform, the transcriptome of P. digitatum treated by Sanxiapeptin was sequenced, and the 6.38 Gb data were analyzed by non-parameter method. The results showed that the cell surface morphology changed significantly after treatment by Sanxiapeptin. Unlike the positive control Bellkute, a membrane-target antifungal, the cell membrane protector of ergosterol significantly alleviated the inhibitory effect of Sanxiapeptin, while the cell wall protector of sorbitol promoted the antifungal ability. The transcriptome alignment rate reached 93.66%, showing high sequencing quality. Sanxiapeptin affected the expression of more than 2000 genes in P. digitatum, which mainly involved in the components of cell membrane and cell wall, autophagy and sugar metabolism. In view of the different pathway from Bellkute, 530 differentially expressed genes caused by Sanxiapeptin alone were analyzed, and these genes were mainly related to the metabolism of hydrophobin, ergosterol, glycan and GPI (glycosylphosphatidylinositol). 17 candidate genes were selected for semi-quantitative expression verification by RT-PCR, among them, 8 genes were completely consistent with the transcriptome sequencing. All the results indicated that Sanxiapeptin could inhibit the postharvest decay fungi in citrus mediated by cell walls or cell membranes.