With the improvement of people's living standards and health care awareness, diabetes, obesity, high blood pressure and other diseases increased year by year the issue has aroused people's attention. The key to solving these problems is to promote the use of high dietary fiber foods. Tartary buckwheat is rich in protein, starch, cellulose, flavonoids and other nutrients, it can improve intestinal microecology, lower blood lipids, prevent colon cancer, treat constipation and lose weight, it can also improve the immunity of human body. Starch, as the main component of tartary buckwheat, has high peak viscosity, high hydration capacity and low solubility. As a natural starch, it has shortcomings such as poor processing ability, narrow range of viscosity and unstable storage performance. Therefore, it needs to be modified to keep the functional characteristics of food to the maximum extent. In recent years, the physical modification method represented by ultra-high pressure, microwave, ultrasonic and other green processing technologies has been applied to starch modification, has become a focus recently. Compared with traditional heat treatment, it has a lower temperature of action. In this paper, the homemade tartary buckwheat starch was treated at 0.1 MPa (ordinary pressure), 100, 200, 300, 400, 500 MPa, and kept for 15 min, using scanning electron microscopy and X-ray diffractometry, etc. analyzed the characteristics of the morphology, crystal structure, solubility, light transmittance and freeze-thaw stability of the tartary buckwheat starch granules. The in vitro model was used to simulate human digestion and intestinal fermentation process. The contents of short chain fatty acids and the main bacterial flora of mouse fecal fermentation broth were determined. The experimental results show that when the pressure was higher than 300 MPa, the surface of tartary buckwheat starch would be inwardly depressed and gradually extruded into a block or sheet and adhered together; and the diffraction intensity was gradually increased (P<0.05). The crystallinity increased from 35.0% to 41.8%. When the pressure reached 500 MPa, the crystal form of tartary buckwheat changed from A to B. Both solubility and expansibility decreased first and then increase with the increase of pressure, and the transmittance would go down, at 200 MPa, the solubility and expansion degree were both the lowest, and the freeze-thaw stability would be improved to some extent. In addition, in the pre-fermentation period (0-8 h), compared with the blank group (without added tartary buckwheat starch)the number of Bifidobacteria and Lactobacilli in the intestinal tract increased significantly after ultra-high pressure treatment (P<0.05) , compared with the blank group (no tartary buckwheat starch was added), the increase of Bifidobacteria in the ultra-high pressure treatment (200 MPa) group and the ultra-high pressure treatment (500 MPa) group was 37.0% and 22.16% respectively. Compared with the blank group, the growth rate of lactobacillus increased by 53.7% in the ultra-high pressure treatment (200 MPa) group, and the growth of Escherichia coli and enterococcus was significantly inhibited (P<0.05). At the same time, the pH value in the intestine decreased significantly (P<0.05). The acetic acid, propionic acid and butyric acid in SCFAs increased significantly (P<0.05), among which, in the early stage of fermentation (0-8 h), the concentration of SCFAs in the ultra-high pressure treatment (200 MPa) group was the highest. That is, tartary buckwheat starch treated with 200 MPa could effectively reduce the pH value of intestinal fermentation fluid and inhibit the growth of harmful bacteria. In a word, after ultra-high pressure treatment, tartary buckwheat can be used as a good natural food for improving intestinal flora.