Cadmium (Cd) is a dangerous pollutant with multiple toxic effects on aquatic animals, and it exists widely in the environment. Selenium (Se) is a biologically essential trace element. Interactions between heavy metals and selenium can significantly affect their biological toxicity, although little is known about the mechanism of this antagonism. Lactobacillus is one of the dominant probiotics, given that a certain dose promotes host health. In this study, we evaluated the protective effect of a dietary probiotic supplementation, Se-enriched Lactobacillus plantarum (L. plantarum), on the bioaccumulation, oxidative stress and gut microflora of Luciobarbus capito exposed to waterborne Cd. Fish were exposed for 28 days to waterborne Cd at 0.05 mg/L and/or dietary Se-enriched L. plantarum. Exposure to Cd in water leads to Cd accumulation in tissues, oxidative stress and significant changes in gut microflora composition. Adding Se-enriched L. plantarum to the diet can reduce the accumulation of Cd in tissues, enhance the activity of antioxidant enzymes, and reverse changes in intestinal microbial composition after Cd exposure. The results obtained indicate that Se-enriched L. plantarum provides significant protection against the toxicity of Cd by inhibiting bioaccumulation. Selenium reduced oxidative stress by increasing the activity of glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX) and malondialdehyde (MDA). Se-enriched L. plantarum can reduce the increase in the number of pathogenic Aeromonas caviae bacteria in the intestine caused by Cd stress and increase the number of Gemmobacter to regulate the microbial population. The results of this study show that Se-enriched L. plantarum dietary supplements can effectively protect Luciobarbus capito against Cd toxicity at subchronic levels.