Objective To investigate the long effect of nonpulsatile flow on changes of structure and function in pulmonary microcirculation and to identify the pulmonary reconstruction under this blood perfusion. Methods Canine models with nonpulsatile flow in the right lung was established, and sacrificed 6 months later. Compare endothelial nitric oxide synthase (eNOS) in vascular endothelium, apoptosis in smooth muscle cell with immunohistochemistry by streptavidinbioepidermmultienzyme complex methodes, and observe structural changes in pulmonary arterioles with optical microscope. Results The expression of eNOS in the right nonpulsatile flow perfusing lung was weaker as compared to the left lung （10 846.7±177.8 vs. 13 136.1±189.6;t＝2.240, P=0.040）, the fas was ber as compared to the left lung（14 254.1±217.1 vs. 11 976.7±195.7; t＝2.160, P=0.040）. The ratio of wall thichness/vessel diameter in the right lung（13.64%±12.80% vs. 14.96%±13.10%） and wall area/vessel area(46.40%±11.70% vs. 47.80%±12.20%) was lower as compared to the left lung(Plt;0.05). Conclusion Longterm nonpulsatile flow can decrease the expression of eNOS, contract the muscles in capillary net, and increase pulmonary vascular resistance. Moreover it canincrease the arteriole apoptosis, leading to vascular structure remodeling.