For image-based computational fluid dynamics (CFD) analysis to characterize the local coronary hemodynamic environment, the accuracy depends on the flow rate which is in turn associated with outlet branches’ morphology. A good flow distribution strategy is important to mitigate the effect when certain branches cannot be considered. In this study, stenotic coronary arteries from 13 patients were used to analyze the effect of missing branches and different flow distribution strategies. Pressure- and wall shear stress (WSS)-derived parameters around the stenotic region (ROI) were compared, including fractional flow reserve (CT-FFR), instantaneous wave-free ratio (CT-iFR), resting distal to aortic coronary pressure (CT-Pd/Pa), time-averaged WSS, oscillatory shear index (OSI) and relative residence time (RRT). Three flow distribution strategies were the Huo-Kassab model at distal outlets (Type I), flow distribution based on outlet resistances (Type II), and a developed algorithm distributing flow at each bifurcation until the final outlets (Type III). Results showed that Type III strategy for models with truncated branch(es) had a good agreement in both pressure- and WSS-related results (interquatile range less than 0.12% and 4.02%, respectively) with the baseline model around the ROI. The relative difference of pressure- and WSS-related results were correlated with the flow differences in the ROI to the baseline mode. Type III strategy had the best performance in maintaining the flow in intermediate branches. It is recommended for CFD analysis. Removal of branches distal to a stenosis can be undertaken with an improved performance and maintained accuracy, while those proximal to the ROI should be kept.