Exposure to titanium dioxide nanoparticles (TiO2 NPs) and bisphenol A (BPA) is ubiquitous, especially through dietary and other environmental pathways. In the present study, adult C57BL/6J mice were exposed to TiO2 NPs (100 mg/kg), BPA (0, 5, and 50 mg/kg), or their binary mixtures for 13 weeks. The 16S rDNA amplification sequence analysis revealed that co-exposure to TiO2 NPs and BPA altered the intestinal microbiota; however, this alteration was mainly caused by TiO2 NPs. Faecal metabolomics analysis revealed that 28 metabolites and 3 metabolic pathways were altered in the co-exposed group. This study is the first to reveal the combined effects of TiO2 NPs and BPA on the mammalian gut microbial community and metabolism dynamics, which is of great value to human health. The coexistence of TiO2 NPs and BPA in the gut poses a potential health risk due to their interaction with the gut microbiota.