This study presents the first bibliometric evaluation and systematic analysis of publications related to mucosal immunity and commensal microbiota over the last two decades and summarizes the contribution of countries, institutions, and scholars in the study of this field. A total of 1423 articles related to mucosal immunity and commensal microbiota in vivo published in 532 journals by 7774 authors from 1771 institutions in 74 countries/regions were analyzed. The interaction between commensal microbiota in vivo and mucosal immunity is essential in regulating the immune response of the body, maintaining communication between different kinds of commensal microbiota and the host, and so on. Several hot spots in this field have been found to have received extensive attention in recent years, especially the effects of metabolites of key strains on mucosal immunity, the physiopathological phenomena of commensal microbiota in various sites including the intestine, and the relationship between COVID-19, mucosal immunity and microbiota. We hope that the full picture of the last 20 years in this research area provided in this study will serve to deliver necessary cutting-edge information to relevant researchers.