Green roofs have been treated as practical low impact development (LID) strategies to retain stormwater runoff and alleviate the rainfall-induced flooding risks in urban regions. The purpose of this study was to analyze the hydrological effects of the spatial location of green roofs in urbanized catchments. In the built-up region of Beijing, 12 urbanized catchments with various architectural patterns were chosen as the study areas. To distinguish the spatial characteristics of roof surfaces, we defined the effective roof surfaces to distinguish from other types of roofs, which have more convenient or direct hydrological connections to drainage systems. A hydrological model was then used to simulate the stormwater mitigation performance of green roofs for the study catchments, which were assigned to different rainfall conditions. The simulation results confirmed the benefits of implementing green roofs for urban stormwater regulation. However, the spatial variability of green roofs showed inherent influences on the runoff mitigation capacity in urbanized catchments. Greening on effective roof surfaces would provide more effective stormwater regulation benefits, for reductions in both runoff volume and peak flow. In addition, the spatial arrangement characteristics of roof surfaces also influenced the hydrological efficiency of green roofs. The effect of the spatial location of green roofs on runoff mitigation was rainfall-dependent. These findings provide insights into the hydrological role of green roofs, and suggest that proper siting of LID facilities should be a consideration for urban stormwater management in order to fulfill the hydrological efficiency and cost-effectiveness planning target.