Atractylodis Rhizoma (AR), a kind of well-known traditional Chinese medicine (TCM), has a long history of being used to treat spleen-deficiency syndrome (SDS). Stir frying with bran is a common method of processing AR, as recorded in the Chinese Pharmacopoeia, and is thought to enhance the therapeutic effect in TCM. Our previous studies have confirmed that bran-fried AR is superior to raw AR in terms of the improvement of gastrointestinal tract function. However, the biological mechanism of action is not yet clear. Here, we report the difference between raw and bran-fried AR in terms of the modulatory effect of intestinal microbiota. We found that the composition of intestinal microbiota of SDS rats changed significantly compared with healthy rats and tended to recover to normal levels after treatment with raw and bran-fried AR. Nine bacteria closely related to SDS were identified at the genus level. Among them, the modulatory effect between the raw and bran-fried AR was different. The improved modulation on Bacteroides, Escherichia-Shigella, Phascolarctobacterium, Incertae-Sedis (Defluviitaleaceae Family) and Incertae-Sedis (Erysipelotrichaceae Family) could be the mechanism by which bran-fried AR enhanced the therapeutic effect. Correlation analysis revealed that the modulation on intestinal microbiota was closely related to the secretion and expression of cytokines and gastrointestinal hormones. These findings can help us to understand the role and significance of bran-fried AR against SDS.