Chinese has experienced unprecedented urbanization over the last several decades. Rapid urbanization led to dramatic increasing of urban impervious surfaces which caused dramatically increasing of the surface runoff and peak flows. Excessive runoff volume coupled with increased peak flow can easily wash accumulated dust off impervious urban surfaces and transport it into receiving water bodies, which can seriously affect public health and threaten environmental quality. The urban non-point source (NPS) pollution has been recognized as a critical cause of water quality degradation and aquatic ecosystem deterioration. In the process of Chinese rapid urbanization, the urban agglomeration has become a new characteristic in urbanization development. Most of urban agglomerations are located in the same watershed. The superimposed effects of the urban NPS pollution caused by cities in a same basin became more and more important, playing one of the key factors restricting the sustainable development of urban agglomeration watershed. The urban NPS pollution have been widely studied at a small city or community scale, few attentions have been paid to watershed scales, especially in an urban agglomeration watershed. In this study, the Central Liaoning Urban Agglomeration in the Hun-Taizi River watershed, was chosen as the study case. The rainfall runoff data was observed in different functional zones and underlying surfaces in Shenyang city. The urban NPS pollutant loads were quantitatively estimated by coupling the event mean concentration (EMC) method and the Storm Water Management Model (SWMM). The results indicated that the EMC values, urban NPS pollutant loads and per unit area yield in road runoff were higher than those in roof runoff and pervious surface. The average annual urban NPS pollutant loads of total phosphorus (TP), total nitrogen (TN), chemical oxygen demand (COD) and total suspended solids (TSS) were 91.01, 280.83, 783.95 and 47212.34 t/a, separately. The average annual urban NPS pollutant loads of cadmium (Cd), nickel (Ni), lead (Pb), chromium (Cr), copper (Cu) and zinc (Zn) were 347.99, 9932.62, 25861.29, 28360.41, 36068.30 and 138840.42 kg/a, separately. Shenyang city had the highest urban NPS pollutant loads while with the lowest per unit area yield of six cities in the Central Liaoning Urban Agglomeration. In this study, a refined approach was presented to accurately estimate the urban NPS pollution by considering the different functional zones, underlying surfaces and rainfall intensities in an urban agglomeration watershed. The method was proposed in this study could provide scientific guidance for urban NPS pollution control and water environment comprehensive management in highly urbanized basins.