Whole-heart sub-millimeter isotropic coronary magnetic resonance angiography (CMRA) provides detailed information of the coronary arteries and surrounding vessels. Recently, a patch-based reconstruction technique (3D PROST) has been proposed to achieve sub-millimeter isotropic resolution CMRA in a predictable scan time. However, this approach only corrects for 2D translational respiratory motion of the heart and image quality can be affected by residual non-rigid motion. Here we propose to integrate 3D PROST into a highly accelerated non-rigid motion correction framework to achieve high quality whole-heart free-breathing isotropic sub-millimeter Cartesian CMRA in a clinically feasible scan time. The feasibility of the proposed method was tested in seven healthy subjects and two patients with suspected coronary artery disease.