Soy hull polysaccharide was extracted by microwave-assisted extractant method， and the effect of soy hull polysaccharide on the rheological properties of simulated intestinal fluid and its regulation on the intestinal flora were investigated. The basic components of soy hull polysaccharide （MOSP） extracted by oxalic acid and soy hull polysaccharide （MCSP） extracted by citric acid were detected. The OD value， pH value and rheological indicator of simulated intestinal fluid were detected after MOSP and MCSP were added to the medium for fermentation. The dynamic changes of intestinal flora were analyzed through Illumina-miseq high-throughput sequencing technology. The results showed that the yield of MOSP was 10.2% and that of MCSP was 5.9%. The purity， moisture and fat content of MOSP were higher than MCSP. The effects of MOSP on promoting intestinal flora proliferation and acid production within 0-24 h was better than that of MCSP. The apparent viscosity of MOSP was the highest at fermentation 24 h. The high-throughput sequencing results showed that both MOSP and MCSP could increase the content of bacteroidetes and firmicutes， and MOSP had a more obvious effect than MCSP. Both soy hull polysaccharides could change the rheological properties and improve the diversity and structural characteristics of the intestinal flora in vitro intestinal simulation system， and the MOSP could achieve better results.