Objective: To explore the difference of intestinal flora between groups of ulcerative colitis and large intestine dampness heat syndrome and healthy group. Methods: A total of 14 stool samples from patients with ulcerative colitis and large intestine dyspepsia syndrome and 14 samples of healthy people were collected. Amplification was designed based on the 16 S r DNA V3-V4 region of the bacteria. Illumina HiSeq 2500 platform was used for high-throughput sequencing.The ultimately sample species information was get by Reads splicing, OTUs (operational taxonomic units) clustering, species annotation, the analysis of alpha diversity and the analysis of principal component. Results: There was a significant difference in intestinal flora between the ulcerative colitis group and the healthy group (P=0.008 ＜ 0.01); and the diversity of intestinal flora in patients with ulcerative colitis and large intestine dyspepsia syndrome was higher than that of healthy people. There a significant difference in the richness degree of intestinal flora patients with ulcerative colitis and large intestine dampness syndrome and the healthy group. Intestinal flora centered on Lactobacillus、Lactobacillaceae、Erysipelotrichaceae、Erysipelotrichales and Akkermansia bacteria was rich in patients with ulcerative colitis. Conclusion: There are significant differences in intestinal flora diversity and bacterial structure between patients with ulcerative colitis and large intestine dampness syndrome and the healthy group.