<p>This study aims to conduct a systematic analysis of the present status, emerging research themes, and evolving trends in the area of gut microbiota–mitochondria interaction in kidney diseases, employing bibliometric methodologies. The literature related to “mitochondria,” “gut microbiota,” and “kidney disease” was retrieved from the Web of Science Core Collection and comprehensively analyzed using R-bibliometrix, CiteSpace, and VOSviewer software. The study included 795 relevant papers published from 2008 to 2025. China, the United States, and Brazil emerged as the most productive countries, with China leading in publication output and the United States exhibiting greater academic influence, as indicated by higher average citation counts. Collaborative efforts are predominantly regional, with limited international cross-border cooperation observed. Mafra Denise from the Federal University of Rio de Janeiro is identified as a core researcher in this domain. Keyword analysis reveals that the research focuses on chronic kidney disease and acute kidney injury, centered around oxidative stress, inflammation, and gut microbiota, The co-occurrence of “mitochondria” as a keyword suggests that studies have progressed from the disease level to cellular and molecular mechanisms. This study employs bibliometric analysis to examine research progress on gut microbiota–mitochondrial crosstalk in the field of kidney disease. By mapping the research landscape at the intersection of microbiota, mitochondria, and kidney disease, it assists researchers in identifying suitable collaborators, journals, and emerging research hotspots and frontiers, thereby providing a reference for future studies in this domain.</p>