Generally, the hemodialysis patient with the prosthetic arteriovenous graft (AVG) undergoes two punctures with needles on the graft in every dialysis session. As an alternative method for patients with AVGs, clinicians and nurses often return the blood filtered by a dialysis machine to an autologous vein not the graft, and that is defined as a separate cannulation method. In this study, we numerically evaluate the influence of the separate cannulation method on the hemodynamics by using clinical information of six patients. In the results, when the separate cannulation method is used, the low time-averaged wall shear stress region increases whereas the high oscillatory shear index region decreases at the venous anastomosis and proximal vein. The quantitative analysis using hemodynamic index indicates the separated cannulation method has pros and cons on the occurrence of complications in AVGs.