PURPOSE: To investigate the differences in gut microbial characteristics between two traditional Chinese syndromes of premature ovarian insufficiency (POI). METHODS: Forty women with POI were recruited from the Department of Traditional Chinese Medicine at Shenzhen Maternity and Child Healthcare Hospital between June and December 2020. Women with POI were divided into the kidney deficiency and blood stasis syndrome (SDBS) and RESULTS: Compared with the QBDS group, the serum levels of estradiol (E2) and anti-Müllerian hormone (AMH) were significantly decreased in the SDBS group. The quantities of Adlercreutzia, Eggerthella, Klebsiella, and Paraprevotella significantly increased in the SDBS group, whereas Lactobacillus decreased significantly. Moreover, alterations in the microbiome in the SDBS and QBDS groups were closely related to the levels of E2 and AMH. The area under the receiver operating characteristic curve for the classification of the two syndromes by the gut microbiome was 0.71. CONCLUSIONS: There were significant differences in the dominant microbiota between the SDBS and QBDS groups, and the change in Proteobacteria in the QBDS group was more significant. The characteristics of gut microbiota help us differentiate between the SDBS and QBDS groups, which may provide a basis for the objectification of TCM syndrome types.