To explore the control effect of ε-polylysine (ε-PL) on postharvest diseases in peach fruits, peach fruits were subjected to inoculation with Monilinia fructicola followed by immersion in ε-PL solutions of different concentrations, or the reverse sequence. The effects of ε-PL on the occurrence and development of brown rot in peach fruits caused by M. fructicola were investigated. The results showed that treatment with 800 mg/L ε-PL alleviated postharvest diseases in peach fruits in both treatments. After storage at 20 ℃ for 2 days, the disease incidence of the first treatment group was 43.3% compared with 73.3% in the control group, indicating that ε-PL significantly decreased the disease incidence of peach fruits. The disease incidence of the second treatment group was 76.7%, 14.8% lower than that of the control group (90%), suggesting that ε-PL treatment enhanced disease resistance. Transcriptome sequencing analysis showed that ε-PL treatment induced differential expression of 825 genes, and these genes were enriched in several pathways such as phenylpropanoid biosynthesis and the biosynthesis of secondary metabolites. Further analysis revealed that ε-PL treatment increased the gene expression levels and activities of phenylalanine ammonia lyase, cinnamate 4-hydroxylase, 4-coumarate-CoA ligase, and peroxidase, thereby promoting the accumulation of total phenols, total flavonoids, and lignin. The above results indicated that ε-PL treatment is an effective method for controlling postharvest diseases of peach fruits. In addition to inhibiting latent pathogens on peach fruits, ε-PL can activate the phenylpropanoid pathway, thereby promoting the accumulation of disease-resistant substances and inducing postharvest disease resistance in peach fruits.