A method for evaluating the sewage collection efficiency of urban sewer network was put forward based on water quality zoning monitoring and the chemical mass balance model. The Bayesian-Markov chain Monte Carlo simulation algorithm was introduced to address the uncertainty problem in source flow proportion simulation, and the reason for the low mass concentration of organic pollution index and poor biodegradability of inflow of wastewater treatment plant was analyzed. Taking the service area of a wastewater treatment plant in Wuhan City as the study site, a site-specific water quality tracer parameter database of domestic sewage, industrial wastewater, and groundwater was established, and in-sewer water quality monitoring along the trunk sewer was carried out. The results showed that by introducing Bayesian-Markov chain Monte Carlo simulation algorithm into the chemical mass balance model, the rational analysis of source flow proportion based on water quality monitoring was realized. The proportion of electronic manufacturing wastewater entering the sewer network was as high as 53.2% to 74.4%, whereas the proportion of infiltrated groundwater was 14.3% to 29.5%. The main reason for the low biodegradability of wastewater treatment plant inflow was associated with large amounts of inorganic industrial wastewater discharge into the sewer network. Therefore, it is necessary to strengthen the surveillance of industrial wastewater discharge, to focus on detection of potential defect in the upstream sewer pipe section, and to improve the efficiency of sewage collection and treatment through targeted measures.