The widespread consumption of nanoplastics (NPs) and bisphenol A (BPA) affected the aquatic ecosystem and imposed risks to the safety of aquatic organisms. This study was aimed at assessing the ecotoxicological effects of single and combined exposure to BPA and polystyrene nanoplastics (PSNPs) on the channel catfish (Ictalurus punctatus). A total of 120 channel catfish were separated into four groups with triplicate (each contains 10 fish) and exposed to chlorinated tap water (control group), PSNP single exposure (0.3 mg/L), BPA single exposure (500 μg/L) and PSNPs (0.3 mg/L) + BPA (500 μg/L) co-exposure for 7 days. Our results showed a relatively higher intestinal accumulation of PSNPs in co-exposure group, compared to PSNP single exposure group. Histopathological analysis showed that single exposure to PSNPs and BPA caused breakage of intestinal villi and swelling of hepatocytes in channel catfish, while the co-exposure exacerbated the histopathological damage. In addition, co-exposure significantly increased SOD, CAT activities and MDA contents in the intestine and liver, inducing oxidative stress. In terms of immune function, the activities of ACP and AKP were significantly decreased. The expressions of immune-related genes such as IL-1β, TLR3, TLR5, hepcidin and β-defensin were significantly up-regulated, and the expression of IL-10 was down-regulated. Additionally, the co-exposure significantly altered the composition of the intestinal microbiota, leading to an increase in the Shannon index and a decrease in the Simpson index. In summary, this study revealed that mixture exposure to PSNPs and BPA exacerbated toxic effects on histopathology, oxidative stress, immune function and intestinal microbiota in channel catfish. It emphasized the threat of NPs and BPA to the health of aquatic organisms and human food safety, with a call for effective ways to regulate the consumption of these anthropogenic chemicals.