Increased accumulation of oxytetracycline (OTC) in environmental water bodies could potentially lead to its accumulation in human body, thereby damaging human intestinal tract. Dietary interventions could be helpful for recovery of intestinal morphology and function. Therefore, this study set zebrafish as model to explore the potential of kefir supplementation in the recovery of intestinal damage caused by exposure to OTC. In experiments by zebrafish, the rearing units used were glass tanks, each with volume of 5 L. The tanks were stocked with 12 zebrafish each. For each treatment, there were 8 replicate tanks. The zebrafish were treated with OTC followed by the addition of kefir to the food. The results showed positive improvements with kefir supplementation. Kefir treatment mitigated intestinal inflammation by reducing the levels of TNF-α, IL-6, and IL-1β; enhancing the activity of the antioxidant enzymes catalase, superoxide dismutase, glutathione peroxidase and increasing the gene expression of intestinal tight junction proteins (ZO-1a and ZO-1b). These effects were beneficial for reversing reduced integrity of intestinal barrier caused by OTC. Moreover, kefir helped to reverse the disruption of gut microbiota caused by OTC and further impacted host metabolism. Specifically, Lactobacillus kefiranofaciens and Lactobacillus kefiri, which were derived from the kefir microbiota, were found to be enriched in the zebrafish intestine. This helped to inhibit the increased abundance of some Proteobacteria species induced by OTC treatment. Liver metabolomics analysis revealed that kefir improved OTC-induced disruptions in the tricarboxylic acid cycle, glycerophospholipid and amino acid metabolism. The differentially abundant metabolites identified included a total of 80 types after OTC exposure, with the abundance of 74 kinds significantly reversed following kefir treatment. Correlation analysis revealed that certain Proteobacteria species and above Lactobacillus species were closely linked with metabolic inhibition in zebrafish caused by OTC and metabolic restoration caused by kefir treatment, respectively.