Background: For treating spleen-deficiency syndrome (SDS), atractylodis rhizoma (AR) is usually treated with bran, which is measured to enhance efficacy. Newly, we found that bran-fried AR (BFA) had benefits over raw AR in refining gut flora. However, the change about metabolism of gut flora caused by raw and BFA remains unclear. Aim: The aim of this study was to compare the difference between raw and BFA acting on short-chain fatty acid (SCFA) metabolism in SDS rats, a metabolic pathway comprising gut flora. Materials and Methods: The model of SDS rats was recognized and then given raw and BFA by gavage. The serum was collected for the determination of motilin (MTL), gastrin (GAS), trypsin (TRY), and amylase (AMS) by enzyme-linked immunosorbent assay. The feces were collected for the determination of 7 SCFAs under selective ion monitoring mode by gas chromatography-mass spectrometer. Results: Raw and BFA can upsurge the levels of MTL, GAS, TRY, and AMS in the serum of SDS rats, diminution the levels of acetic acid and propionic acid, and rise the level of hexanoic acid in the feces of SDS rats, and BFA showed noteworthy activity than raw AR. Conclusion: Raw and BFA can improve the acetic acid, propionic acid, and hexanoic acid metabolism in SDS rats, and BFA was more potent than raw AR.