For the purpose of analyzing and managing Urban Water Pollution Discharge Systems (UWPDS) comprehensively, a systematic approach of tracking and tracing analyses was developed based on environmental systems analysis theory, in which the directed graph, the nodal flow balance and the network analysis of Geographic Information System (GIS) were used. Based on the digitalized UWPDS of GIS which was established by collecting and processing a large amount of topographic, sewage discharge and drainage data, this scientific approach can be applied to make the tracking and tracing analyses on wastewater treatment plants, pumping stations, illicit sewage outlets, pollution sources and drainage pipelines systematically. The upstream and downstream information about sources, discharging paths, flow quantities and final destinations of pollutants was obtained, and potential problems in the UWPDS analysis such as illicit connections between different drainage pipelines were identified, with the spatial analysis. This developed approach was tested using the UWPDS of Chaohu City (Anhui Province, China). The study results are important for the implementation of sewage interception engineering, the determination of load reduction, and the optimization of drainage pipelines and pumping stations in future.