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Aims This study aimed to conduct a bibliometric analysis of the relevant literature on the interaction between microbiota and immune in intestinal inflammatory diseases, and show its current status, hotspots, and development trends. Methods The related literature was acquired from the Web of Science Core Collection on October 12, 2022. Co-occurrence and cooperation relationship analysis of authors, institutions, countries, references, and keywords in the literature were carried out through CiteSpace 6.1.R3 software and the Online Analysis platform of Literature Metrology. At the same time, the relevant knowledge maps were drawn, and the keywords cluster analysis and emergence analysis were performed. Results 3,608 related publications were included, showing that the number of articles in this field is increasing year by year. The results showed that Gasbarrini A and Sokol H were the authors with the highest cumulative number of articles with 25, and the institution with the most articles was Harvard University with 142 articles. The USA was far ahead in the article output, with 1,131 articles, and had a dominant role, followed by China with 707 articles. The journal Frontiers in Immunology contributed the most to this research field with 213 articles. In the cooperation network analysis, the USA, Harvard University, and Xavier RJ were the most widely collaborated country, institution, and author, respectively, which implied a high level of influence. Keywords analysis showed that there were 770 keywords, which were mainly classified as internal related diseases, such as “inflammatory bowel disease”, “irritable bowel syndrome”, “colorectal cancer”, and the mechanism of interaction of microbiota and immune, such as “intestinal microbiota”, “commensal microbiota”, “regulatory T cell”, “dendritic cell”, “barrier function”, “activation”, “anti-inflammatory properties”, “intestinal epithelium”, and “diversity”. Emerging analysis showed that future research hotspots and trends might be the short-chain fatty acid, gut dysbiosis, gut-liver axis, and fusobacterium nucleatum. Conclusion This research was the first bibliometric analysis of publications in the field of interaction between microbiota and immune in intestinal inflammatory diseases using visualization software and data information mining, and obtained the current status, hotspots, and development of this field, which provides a theoretical basis for its scientific research.