Abstract: Changes in the abundance and types of gut microbiome can lead to diseases, and many basic and nervous system diseases have been confirmed to be related to gut microbiome. Exploring the molecular pathogenic mechanism of gut microbiome is the basis of directed regulation of gut microbiome to cure diseases. In this review, four molecular pathogenic mechanisms, including metabolic disorder caused by functional gene difference in gut microbiome, inflammatory cascade caused by proinflammatory factors, immune cell differentiation mediated by flora, and brain gut axis affecting brain activity are summarized. A "top-down" research approach, beginning with association analysis to molecular mechanism investigation is proposed, and nutritional intervention strategies developed for the corresponding pathogenic mechanisms are also summarized. In the future, the pathogenic mechanism of gut microbiome can be further studied employing the "top-down" approach, and nutritional intervention can be carried out more accurately basing on the relative pathogenic mechanism.