Naringin (NAR) is a dihydroflavonoid with various biological activities and pharmacological effects, especially natural antioxidant activity. To gain a better understanding of the effects of NAR on the reproductive system, especially spermatogenesis, we employed western blotting, immunofluorescence, immunohistochemistry, metabolomics and microbiomics to comprehensively dissect the impact of NAR on spermatogenesis. NAR promotes germ cell proliferation and testicular development, and promotes the secretion of sex hormones. Microbiomic and metabonomic analysis showed that NAR improved intestinal microflora and cooperated with serum metabolites to regulate spermatogenesis. Therefore, NAR is beneficial for male reproduction by regulating intestinal microorganisms and serum metabolism.