Currently, gut microbiota living in the gastrointestinaltract, plays an important role in regulatinghost’s sleep and circadian rhythms. As a tool, gut microbiotahas great potential for treating circadian disturbanceand circadian insomnia. However, the relationship betweengut microbiota and circadian rhythms is still unclear, andthe mechanism of action has still been the focus ofmicrobiome research. Therefore, this article summarizesthe current evidences associating gut microbiota with factorsthat impact host circadian rhythms neurology sleepdisorder. Moreover, we discuss the changes to these systemsin sleep disorder and the potential mechanism ofintestinal microbiota in regulating circadian rhythms neurologysleep disorder via microbial metabolites. Meanwhile,based on the role of intestinal flora, it is provided anovel insight into circadian related insomnia and will bebenefit the dietary treatment of circadian disturbance andthe circadian related insomnia.