Waste is increasingly used as a renewable resource. Industrial symbiosis is an innovative concept for more efficient use of waste streams within industrial complexes, with the aim of reducing the overall environmental impact of the complex. Industrial symbiosis plays a more important role in promoting green economic growth and building low-carbon cities. Based on the ecological theoretical framework, combined with Waste Flow Analysis (WFA), the material flow analysis (MFA) and production matrix methods were used as the core to construct the Industrial Symbiosis System Waste Flow Metabolism Analysis (ISSWFMA) model. In addition, taking the “Jinchang Model” as an example, a typical case selected by the National Development and Reform Commission of China’s regional circular economy development model, we conducted a refined quantitative study on the flow and metabolism of waste flow in the regional industrial symbiosis system at the City-Region level using the circulation degree index. The following conclusions were obtained from the study: The ISSWFMA model can better describe the flow and metabolism of waste streams in the industrial symbiosis system at the City-Region Level and can provide data and methods for storage management. As the internal industrial chain and the correlation between various departments continuously improved, the Circulation Index (CI) of solid waste, wastewater, and exhaust gas in the industrial symbiosis system of Jinchang City showed an overall increasing trend, the degree of recycling was continuously increasing, the industrial symbiosis ability was continuously enhanced, and the system structure was more complete. At the same time, based on the analysis of different wastes, the industrial symbiosis is developed at different stages; based on the analysis of solid wastes, the industrial symbiosis ability of Jinchang’s Industrial Symbiosis System has strengthened and accelerated the fastest from 2005 to 2010; based on the analysis of wastewater, the industrial symbiosis ability of the system strengthened slowly during the whole study period; and based on the analysis of exhaust gas, the industrial symbiosis ability of the system continued to strengthen rapidly during the whole study period. Finally, on the basis of further discussion on the selection of waste recycling paths, we proposed to give full play to the role of market mechanisms, and to build recycling areas and ecological areas by strengthening industrial symbiosis and its derived urban symbiosis to achieve the goals of natural resource conservation, ecological environment protection, and harmonious coexistence between human and nature.