The interaction between host circadian rhythm and gut microbes through the gut-brain axis provides new clues for tea polyphenols to improve host health. Our present research showed that oolong tea polyphenols (OTP) improved the structural disorder of the intestinal flora caused by continuous darkness, thereby modulating the production of metabolites related to pyruvate metabolism, glycolysis/gluconeogenesis, and tryptophan metabolism to alleviate the steady-state imbalance. After fecal microbiota transplantation from the OTP group, the single-cell transcriptomic analysis revealed that OTP significantly increased the number of hypothalamus cell clusters, up-regulated the number of astrocytes and fibroblasts, and enhanced the expression of circadian rhythm genes Cry2, Per3, Bhlhe41, Nr1d1, Nr1d2, Dbp and Rorb in hypothalamic cells. Our results confirmed that OTP can actively improve the intestinal environmental state as well as internal/peripheral circadian rhythm disorders and cognitive impairment, with potential prebiotic functional characteristics to notably contribute to host health.