Automated identification and tracking of mesoscale ocean eddies has recently become one research hotspot in physical oceanography. Several methods have been developed and applied to survey the general kinetic and geometric characteristics of the ocean eddies in the South China Sea(SCS). However, very few studies attempt to examine eddies’ internal evolution processes. In this study, we reported a hybrid method to trace eddies’ propagation in the SCS based on their internal structures, which are characterized by eddy centers, footprint borders, and composite borders. Eddy identification and tracking results were represented by a GIS-based spatiotemporal model. Information on instant states, dynamic evolution processes, and events of disappearance, reappearance, split, and mergence is stored in a GIS database. Results were validated by comparing against the ten Dongsha Cyclonic Eddies(DCEs) and the three long-lived anticyclonic eddies(ACEs) in the northern SCS, which were reported in previous literature. Our study confirmed the development of these eddies. Furthermore, we found more DCE-like and ACE-like eddies in these areas from 2005 to 2012 in our database. Spatial distribution analysis of disappearing, reappearing, splitting, and merging activities shows that eddies in the SCS tend to cluster to the northwest of Luzon Island, southwest of Luzon Strait, and around the marginal sea of Vietnam. Kuroshio intrusions and the complex sea floor topography in these areas are the possible factors that lead to these spatial clusters. Automated identification and tracking of mesoscale ocean eddies has recently become one research hotspot in physical oceanography. Several methods have been developed and applied to survey the general kinetic and geometric characteristics of the ocean eddies in the South China Sea (SCS). However, very few studies attempt to examine eddies ’internal evolution processes. we reported a hybrid method to trace eddies’ propagation in the SCS based on their internal structures, which are characterized by eddy centers, footprint borders, and composite borders. tracking results were represented by GIS-based spatiotemporal model. Information on instant states, dynamic evolution processes, and events of disappearance, reappearance, split, and mergence is stored in a GIS database. Results were validated by comparing against the ten Dongsha Cyclonic Eddies (DCEs) and the three long-lived anticyclonic eddies (ACEs) in the northern SCS, which were reported in pre vious literature. Our study confirmed the development of these eddies. Our, we found more DCE-like and ACE-like eddies in these areas from 2005 to 2012 in our database. Spatial distribution analysis of disappearing, reappearing, splitting, and merging activities shows that eddies in the SCS tend to cluster to the northwest of Luzon Island, southwest of Luzon Strait, and around the marginal sea of ​​Vietnam. Kuroshio intrusions and the complex sea floor topography in the possible factors that lead to these spatial clusters.