Objective To establish a method for non-invasive calculation of fractional flow reserve (FFRCT) with the shape resistance of coronary artery stenosis as boundary condition, and to verify the accuracy of this method. Methods CT angiography images of 16 patients with coronary artery disease were reconstructed; the mathematical model of shape resistance was established by considering the minimum cross sectional area and the length of stenosis of coronary artery stenosis, the induced pressure difference as the boundary condition was applied to calculate FFRCT (named as shape resistance method). The values of clinical FFR were taken as the gold standard, previous diameter method and volume method were taken as control methods, and accuracy of shape resistance method was investigated from the aspects of mean error rate, accuracy rate, sensitivity rate, positive prediction rate and negative prediction rate. Results The mean error rate of calculated FFRCT by the diameter method, volume method and shape resistance method were 11.76%, 10.46%, 4.82%, accuracy rate were 85%, 65%, 90%, the sensitivity rate were 87.5%, 66.7%, 87.5%, positive prediction rate were 75%, 25%, 87.5%, respectively, while negative prediction rate were all 91.6%. Conclusions The established shape resistance method is better than the diameter method and volume method from the aspects of mean error rate, accuracy rate, sensitivity rate and positive prediction rate; the FFRCT based on the shape resistance method and clinical FFR have good consistency, and this work may provide a new way for the calculation and application of FFRCT.