Abstract: Establishing corresponding features on two non-rigidly deformed 3D surfaces is a challenging and well-studied problem in computer graphics. Unlike previous approaches that constrain the matching between feature pairs using isometry-invariant distance metrics, we constrain the matching using a discrete connectivity graph derived from the Morse-Smale complex of the Auto Diffusion Function. We observed that the graph remains stable even for surfaces differing by topology or by significant deformation. This algorithm is simple to implement and efficient to run. When tested on a range of examples, our algorithm produces comparable results with state-of-art methods on surfaces with strong isometry but with greatly improved efficiency, and often gets better correspondences on surfaces with larger shape variances.