Processing techniques have been shown to alter the nutritional composition of rice bran (RB) and wheat bran (WB), influencing their ability to modify microbial, but a systematic comparison is currently lacking. This study aimed to comprehensively investigate the effects of various processing methods, including physical modifications (grinding, extrusion, steam explosion), enzymolysis (amylase, hemicellulose, and xylanase), and union modifications, on the modification of gut microbiota by RB and WB. Processing methods significantly altered the nutrient components of RB and WB as well as their capacity for gas and SCFA production during in vitro fermentation. The RB23 (amylase treatment), RB31(extrusion and hemicellulose treatment), and RB33 (steam explosion and xylanase treatment) samples exhibited the highest production of total SCFAs and butyric acid during in vitro fermentation. Overall, the microbiota responses to brans were conserved within individuals and processing methods explained 21.6% of the variance. Fermentation of RB23, RB31, and RB33 samples was observed to enhance the richness of gut microbiota, decrease the Firmicutes/Bacteroidetes ratio, and stimulate the growth of Butyricicoccus and Faecallbacterium while inhibiting the growth of Bilophila, Fusobacterium, and Escherichia-shigella. The findings from this study may provide valuable insights for the processing of RB and WB.