Objective To examine the changes of ultrastructural microcirculation of small intestines of portal hypertension (PHT) canines. Methods PHT canine models were established by coarcating a half main portal vein with silk line chronic emboliztion. The ultrastructural changes of small intestine epithelium, mucous membrane and submucosa microcirculation were examined. Results The characteristics of ultrastructural changes of small intestine epithelium, mucous membrane and submucosa microcirculation were as follows: the number of blood vessels was increased and the diameter of them was expanded significantly; the lumen of arteriole was decreased, and the wall was thickened; arteriole collagen fibers were hyperplastic and confused; the lumen of venule was increased, the wall was thinned; basement membrane was damaged; microcirculatary endothelial cell was damaged generally; leukocytes was infiltrated; epithelial cells and basement membrane of intestinal mucosa were damaged; smooth muscle cell nucleus of ileum were deformed. Conclusion Small intestine epithelium, mucous membrane and submucosa microcirculatary ultrastructral showed obvious changes in PHT canines.