To assess the performance of urban drainage systems in metropolitan areas in southern China, 12 urban drainage systems, including nine separate sewer systems (SSSs) and three combined sewer systems (CSSs) were monitored from 2008 to 2012 in Shanghai and Hefei. Illicit connection rates of SSS were determined. The results indicate that serious illicit connections exist for most SSSs. Annual volume balance for two SSSs with serious illicit connection was assessed with a hydraulic model to determine the dry weather overflow volume. Although interception facilities have been implemented in SSSs, for some systems with serious illicit connections, a considerable volume of dry weather overflow still existed. Combined with monitoring of dry/wet weather flow quality, the pollutant load caused by wet/dry weather overflow was quantified. The results revealed that there was no obvious advantage of having SSSs over CSSs in terms of pollutant control. The serious pollution caused by illicit connections and insufficient management occurs in many cities in China. The performance assessment of separate and CSSs in Shanghai and Hefei provides important lessons and practical experience that can be applied to the construction and management of urban drainage system in China as well as other developing countries.