This study provides a comprehensive bibliometric analysis of the research trends and hotspots in the field of gut microbiota and epigenetics. The analysis was conducted using data from the Web of Science Core Collection (WoSCC) database, with Vosviewer 1.6.17 and CiteSpace 6.1.R2 for visualization and quantitative analysis. The results show that the number of publications on gut microbiota and epigenetics has been increasing annually since 2011, with a peak in 2022 and 2023. The United States, China, and Italy are the leading countries in this field, with the University of California System, Harvard University, and the University of London being the top research institutions. Li, X, Yu, Q, and Zhang, S X are the most prolific authors. The current research hotspots include the role of short-chain fatty acids (SCFAs) in gut microbiota and epigenetic mechanisms, the impact of gut microbiota and epigenetics on host obesity, diet, and metabolism, and their close relationship with colorectal cancer, breast cancer, and inflammatory bowel disease. Additionally, the study highlights the gut-brain axis as a key regulatory mechanism, where gut microbiota can influence epigenetics and psychiatric diseases. Probiotics are suggested to regulate gut microbiota, improve lifestyle, and reduce the occurrence and development of diseases. The study concludes that bibliometric analysis provides valuable insights into the research trends and directions in the field, guiding future research efforts.This study provides a comprehensive bibliometric analysis of the research trends and hotspots in the field of gut microbiota and epigenetics. The analysis was conducted using data from the Web of Science Core Collection (WoSCC) database, with Vosviewer 1.6.17 and CiteSpace 6.1.R2 for visualization and quantitative analysis. The results show that the number of publications on gut microbiota and epigenetics has been increasing annually since 2011, with a peak in 2022 and 2023. The United States, China, and Italy are the leading countries in this field, with the University of California System, Harvard University, and the University of London being the top research institutions. Li, X, Yu, Q, and Zhang, S X are the most prolific authors. The current research hotspots include the role of short-chain fatty acids (SCFAs) in gut microbiota and epigenetic mechanisms, the impact of gut microbiota and epigenetics on host obesity, diet, and metabolism, and their close relationship with colorectal cancer, breast cancer, and inflammatory bowel disease. Additionally, the study highlights the gut-brain axis as a key regulatory mechanism, where gut microbiota can influence epigenetics and psychiatric diseases. Probiotics are suggested to regulate gut microbiota, improve lifestyle, and reduce the occurrence and development of diseases. The study concludes that bibliometric analysis provides valuable insights into the research trends and directions in the field, guiding future research efforts.