In order to quickly and accurately trace the source of water pollution when the water quality of monitoring section exceeded the standard, a spatial relationship model of basin elements for water pollution traceability was proposed by integrating existing river basin elements. The model was based on four levels of river reach and catchment unit, and established the coding relationship between catchment unit level and upstream and downstream river reach. Then it established the spatial correlation relationship between the whole basin elements and catchment unit, and constructed five subsystem models of the spatial relationship of basin elements. Finally, the subsystem models were aggregated to form a collaborative spatial relationship network of river basin elements. Taking the real-time water quality monitoring section of Aojiang River Basin as the trigger point of pollution traceability, the subsystem model of spatial relationship of elements in each basin was directly applied to the process of water pollution traceability. The results show that the established relationship model can provide the spatial distribution and structure information of pollution sources to the greatest extent in practical application, effectively identify and screen the water pollution sources in the study area, quickly reduce the search scope of unknown pollution sources, and improve the efficiency and accuracy of water pollution traceability search process.