Inflow and infiltration of a sewage system was estimated by synthetic model. Homological feature of catchments was recognized by self-organizing map. Occurrence risk index was proposed to assess catchment operation problem. Optimal strategy was used to reduce surcharge events and improve effluent quality. Inflow and infiltration (I/I) are serious problems in hybrid sewerage systems. Limited sewerage information impedes the estimation accuracy of I/I for each system catchment because of its unknown distribution. A new method proposed to deal with I/I of a large-scale hybrid sewerage system with limited infrastructure facility data is presented in this study. The catchment of representative pump stations was adopted to demonstrate the homological catchments that have similar wastewater fluctuation characteristics. Homological catchments were clustered using the self-organizing map (SOM) analysis based on long-term daily flow records of 50 pumping stations. An assessment index was applied to describe the I/I and overflow risk of representative pump stations in the catchment based on the hourly wastewater quality and quantity data. The potential operational strategy of homological catchments was generated by the assessment index of representative pump stations. The simulation results of the potential operational strategy indicated that the optimized operation strategy could reduce surcharge events and significantly improve the quality of wastewater treatment plant effluent.