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Bisphenol A (BPA) is an endocrine disruptor, widely employed, and detected in many consumer products and food items. Oral intake poses a great threat to intestinal health. Melatonin (MT) stands out as an endogenous, dietary, and therapeutic molecule with potent antioxidant capacity. To explore the protective effect of MT against BPA-induced colon damage and the role of NADPH oxidase (NOX) in this process, we established mice and colonic epithelial cell (NCM460) models of BPA exposure and treated with MT. In vitro and in vivo results showed that MT ameliorated BPA-induced oxidative stress, DNA damage, and the G2/ M cell cycle arrest. MT also downregulated the expression of NOX family-related genes, reversed the inhibition of the base excision repair (BER) pathway, promoted the activation of non-homologous end-joining (NHEJ) pathway, and suppressed the mRNA and protein expression of ATM, Chk1/2, and p53. Diphenyleneiodonium chloride (DPI), a NOX-specific inhibitor, also attenuated the toxic effects of BPA on NCM460 cells. Furthermore, molecular docking revealed that MT could bind to NOX. Conclusively, our finding suggested that MT can ameliorate BPA-induced colonic DNA damage by scavenging NOX-derived ROS, which further attenuates G2/M cell cycle arrest dependent on the ATM-Chk1/2-p53 axis.