BACKGROUND: In recent years, the relationship between gut microbiota and human health has garnered significant attention. Notably, the potential connection between gut microbiota and mental health issues, such as depression and anxiety, has emerged as a new focal point for research. While some studies suggest a possible link between these factors, the field remains in its early stages of development, and there are notable methodological and sample size limitations. PURPOSE: This study aims to systematically summarize the knowledge systems, research hotspots, and development trends related to intestinal microflora within the context of depression research. METHODS: This study conducted a search for publications related to intestinal microflora and depression in the Web of Science Core Collection (WOSCC) prior to August 6, 2024. The selected literature was subsequently analyzed using VOSviewer (v.1.6.20), SCImago Graphica (v.1.0.39), and CiteSpace (v.6.3.1). RESULTS: The study encompassed a total of 1,046 publications, demonstrating a consistent increase in annual publication volume. The primary research countries identified are China and the United States, with notable contributions from institutions such as the University of California and University College Cork, among others. Keywords analysis highlighted high-frequency terms including "gut microbiota," "depression," and "anxiety," and revealed 10 keyword clusters along with 20 strongest citation bursts keywords. The focus of research has shifted from compositional analysis of gut microbiota to its role in the pathogenesis of depression. CONCLUSIONS: Research on gut microbiota and depression is growing, but there is still a need for greater collaboration between authors and institutions across regions, more ongoing interaction and communication to further explore the mechanisms of action of gut microbiota, to develop microbiota-based interventions, and to facilitate translation of research findings into clinical practice.