Objective To observe the influence of Shenlingbaizhusan on intestinal flora of rats modeled by ulcerative colitis（UC）of spleen deficiency and dampness type in order to explore the therapeutic mechanism of Shenlingbaizhusan to UC. Methods 40 healthy Wistar rats were randomly divided into normal group，model group，Shenlingbaizhusan treated group，and sulfasalazine（SASP）group. The damp-heat syndrome of stomach and intestine were copied by multivariate methods which simulated the etiology of Traditional Chinese Medicine. The treatment had been given to the appropriate model. Total bacterial DNA was extracted from the contents of the colon. Flora was analyzed by ERIC-PCR technology. Results There were the differences of the intestinal flora in four groups according to the analysis. The DNA bands of ERIC-PCR fingerprinting electrophoresis were little in model group. The DNA bands of ERIC-PCR fingerprinting electrophoresis were numerous in other three groups. The trend of main-belt location of Shenlingbaizhusan was close to normal group. Conclusion There might be an advantage intestinal bacterium. Shenlingbaizhusan played an important role in adjusting microflora imbalance of UC of spleen deficiency and dampness type,Increasing dominant strain of intetinal,restoring the flora balance status in order to promote the recovery of damaged intestinal tissue.