Previous studies suggested that the reconstruction or maintenance of physiological blood flow paths in the heart is important in order to obtain a good outcome following cardiac surgery, but this concept has no established theoretical foundation. We developed a multi-scale, multiphysics heart simulator, based on the finite element method, and compared the hemodynamics of ventricles with physiological (P) and non-physiological (N) flow paths. We found that the physiological flow path did not have an energy-saving effect, but facilitated the separation of the outflow and inflow paths, so avoiding mixing of the blood. The work performed by the ventricular wall was comparable at slower and faster heart rates (P vs. N: 0.864 vs.0.874 J (heart rate (HR)=60 beats/min), 0.599 vs. 0.590 J (HR=100 beats/min)) indicating that chiral asymmetry of the flow paths in the mammalian heart has minimal functional merit. At lower heart rates, the blood coming in the first beat was cleared almost completely by the ninth beat in both models. However, at high heart rates, such complete clearance was observed only in the physiological model, whilst 27.0% of blood remained in the non-physiological model. This multi-scale heart simulator provided detailed information on the cardiac mechanics and flow dynamics, and could be a useful tool in cardiac physiology.