This study aims to apply a CCTA-derived territory-based patient-specific estimation of boundary conditions for coronary artery fractional flow reserve (FFR) and wall shear stress (WSS) simulation. The non-invasive simulation can help diagnose the significance of coronary stenosis and the likelihood of myocardial ischemia. FFR is often regarded as the gold standard to evaluate the functional significance of stenosis in coronary arteries. In another aspect, proximal wall shear stress ([Formula: see text]) can also be an indicator of plaque vulnerability. During the simulation process, the mass flow rate of the blood in coronary arteries is one of the most important boundary conditions. This study utilized the myocardium territory to estimate and allocate the mass flow rate. 20 patients are included in this study. From the knowledge of anatomical information of coronary arteries and the myocardium, the territory-based FFR and the [Formula: see text] can both be derived from fluid dynamics simulations. Applying the threshold of distinguishing between significant and non-significant stenosis, the territory-based method can reach the accuracy, sensitivity, and specificity of 0.88, 0.90, and 0.80, respectively. For significantly stenotic cases ([Formula: see text] [Formula: see text] 0.80), the vessels usually have higher wall shear stress in the proximal region of the lesion.