The paper presents a geographical information system (GIS)-based method for depicting the characteristics, particularly the internal structures and evolutionary processes, of mesoscale eddies. This was done by examining topologic relations among closed sea surface height (SSH) contours that were reconstructed from the Naval Research Laboratory Navy layered ocean model (NLOM). Different scenarios of the topological relations among the contour lines permitted the identification of the outermost outline of eddies and the depiction of the number of cores in each mesoscale oceanic eddy. With full consideration of the internal structure of the eddies, we then reconstructed the evolutionary processes of these eddies, and the results were compared with empirical observations on three long-lived mesoscale eddies in the northern South China Sea (SCS). Tracking results were similar, thereby validating our method as being efficient and robust in reconstructing mesoscale ocean eddies, especially their evolutionary processes based on their internal structures.