Kiwifruit has high economic value but is susceptible to fungal infection after harvest. Botrytis cinerea (B. cinerea) is one of these fungal pathogens that cause huge economic losses and potential food safety problems. Auxin is a vital plant growth regulator that has been reported to play a role in plant defense. In this study, postharvest kiwifruit was treated with different concentrations of indole-3-acetic acid (IAA), after which the average incidence rate and lesion area were analyzed to determine the appropriate concentration of IAA for disease resistance. Defense enzymes, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were detected. Ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS)-based widely targeted metabolomic analysis was used to investigate the mechanism of kiwifruit active compounds during IAA treatment and B. cinerea infection. Exogenous IAA treatment (especially at 50 μg/ mL) enhanced the resistance of kiwifruit to B. cinerea, resulting in reduced disease incidence and lesion area, and showed higher pathogen resistance-related defense enzyme activity in response to B. cinerea infection. Further metabolomic analysis revealed 776 metabolites in kiwifruit after IAA treatment, among which 51 metabolites in IAA_24h (24 h after IAA treatment) vs. CK (sterilized ddH2O treatment) fruit, 55 metabolites in IAA_72h (72 h after IAA treatment) vs. CK, and 67 metabolites in IAA_24h vs. IAA_72h were found to be significantly different. KEGG analysis showed that the resistance induced in kiwifruit by IAA treatment was closely related to the activation of phenylpropanoids, including flavonoids and phenols, terpenoids, carbohydrate metabolism, and hormone signaling pathways. These results might reveal the mechanism of IAA-induced resistance in kiwifruit and provide a new theoretical basis for the safe and efficient control of postharvest diseases in kiwifruit.