Nectarine fruits are rich in nutrients, which are susceptible to fungal infection during postharvest, resulting in quality deterioration and decay. This study aimed to assess the effect of different concentrations of carvacrol and soy protein isolate coatings on the fungal infection and quality characteristics of nectarines during postharvest storage. The results showed that soy protein isolate carvacrol (SPI-C) coating inhibited the growth of Rhizopus stolonifer in vitro. The SPI-C coating significantly reduced the incidence of postharvest soft rot, maintained the postharvest quality of nectarines during storage. SPI-C coating induces the defense response to soft rot by enhancing the accumulation of phenolic, flavonoids and lignin, and up-regulating the expression of defense-related genes in nectarines. The SPI-C coating activated the transcription of antioxidant enzymes (CAT, SOD and POD) and eliminated ROS damage. The disease resistance response promotes the production of defense-related substances by upregulating the gene expression of PpPPO and PpPAL. In summary, SPI-C coating significantly reduces the incidence of postharvest soft rot, maintains the postharvest quality and induces defense response to soft rot by enhancing the expression of genes involved in phenylpropanoid metabolism in nectarines during storage.