Under the control of the host circadian rhythms, intestinal microbiota undergoes dietary-dependent diurnal fluctuations in composition and function. In addition, microbiome plays a critical role in maintaining the host circadian rhythms and metabolic homeostasis. The interactions between host circadian rhythms and intestinal microbiota suggest that intervention with prebiotics or probiotic is a possible way to alleviate circadian rhythm misalignment and related metabolic diseases. This review discusses the circadian rhythm oscillations of gut flora, relationship between host circadian rhythms and microbiome and related effects on metabolism. The influence on circadian rhythms by the interactions between tea polyphenols (TP) and intestinal microbiota is highlighted.