BACKGROUND: Bibliometric analysis is an approach to evaluate the circumstances and trends in specific research field over time and to provide inspiration in future research and policy. Researches have a tremendous increase focus on the role of the microbiota in the development of diabetes in recent years; however, there is no published literature conducting a bibliometric analysis to explore the tendency. The aim of this study was to provide a detailed evaluation of the hundred most cited articles in microbiota of diabetes research. METHODS: The database of the Web of Science was utilized for identification of articles. The top 100 were selected for further analysis of authorship, number of citations, article type, source journal, geographic origin, and interactions. RESULTS: The articles selected were published from 2007 to 2015. The total citations ranged from 1289 to 35, citation density ranged from 163.75 to 6.5. The article type included basic science (n = 32), review (n = 29), expert opinion (n = 19), cross-sectional study (n = 12), RCT (n = 3), and others (n = 5). The study content included pathogenesis (n = 58), risk factor (n = 11), modifying of intestinal microbiota (n = 10), prebiotic treatment (n = 8), antibiotic treatment (n = 4), diet control (n = 4), and others (n = 5). The 100 most cited articles were published in 59 journals. Among them, Diabetes (n = 7), Diabetologia (n = 7), and Plos one (n = 7) published the most T100 articles. In total, 24 countries and 174 scientific research institutions participated in those researches. USA (n = 32) and Belgium (n = 22) were the leading countries in this field, followed by France (n = 18) and Finland (n = 16). Patrice D. Cani contributed the most top cited articles (n = 15). CONCLUSION: This bibliometric study is likely to include a list of intellectual milestones focused on microbiota of diabetes research in the past decade, which provides insights into the circumstances and trends in preventing and treating diabetes from a new perspective.