Insomnia is a type of sleep disorder which has negative impacts on the quality of life, mood, cognitive function and health of humans. The etiology of insomnia may be related to many factors such as genetics, biochemistry, neuroendocrine, immune, and psychosocial factors. However, the detailed pathological aspects of insomnia remain unclear. Recent investigation of the microbiome–gut–brain axis enhances our understanding of the role of the gut microbiota in brain-related diseases. Gut microbiome has been shown to be associated with insomnia. However, the available data in this field remain limited and the relevant scientific work has only recently begun. This review aims to summarize the recent literature as an aid to better understanding how the alteration of gut microbiota composition contributes to insomnia while evaluating and prospecting the therapeutic effect of modulating gut microbiota in the treatment of insomnia based on previous publications.