Background: Herbal medicine is a low-cost treatment and has been increasingly applied in obesity treatment. Gut microbiota (GM) is strongly associated with obesity pathogenesis. Methods: We conducted a systematic review guided by the question: “Does the use of herbal medicine change the GM composition in obese individuals?” Randomized clinical trials with obese individuals assessing the effects of herbal medicine intervention in GM were retrieved from the Medline, Embase, Scopus, Web of Science, and Cochrane Library databases, including the Cochrane Controlled Trials Register. Two reviewers independently extracted data using standardized piloted data extraction forms and assessed the study-level risk of bias using an Excel template of the Cochrane “Risk of bias” tool 2—RoB 2. Results: We identified 1094 articles in the databases. After removing duplicates and reading the title and abstract, 14 publications were fully evaluated, of which seven publications from six studies were considered eligible. The herbs analyzed wereMoringa oleifera,Punica granatum,Scutellaria baicalensis,Schisandra chinensis, W-LHIT and WCBE. The analysis showed thatSchisandra chinensisandScutellaria baicalensishad significant effects on weight loss herbal intervention therapy composed by five Chinese herbal medicinesGanoderma lucidum,Coptis chinensis,Astragalus membranaceus,Nelumbo nucifera gaertn, andFructus aurantii(W-LHIT) and white common bean extract (WCBE) on GM, but no significant changes in anthropometry and laboratory biomarkers. Conclusions: Herbal medicine modulates GM and is associated with increased genera in obese individuals.