The rapid urbanization has increased the impervious surface of cities, seriously affecting urban water security. Study of hydrological performance of green roofs is of great significance to urban water security and sustainable development, especially in areas of highly urbanization where land resources are scarce and environmental problems are prominent. However, there are still few studies on the hydrological performance of green roofs within a city range. In this study, a typical highly urbanizing area of 142 km² of Xiamen Island was chosen as a case study. Under four green roofs implementation scenarios of the return period (2, 5, 10, and 20 years), the hydrological performance of green roofs was investigated by the ArcGIS and Soil Conservation Service Curve Number (SCS-CN) model. The differentiated ecological construction strategies were formulated according to its spatial differentiation characteristics. The results show that (1) the average runoff reduction rates increase from 0.91% to 4.51% with the increasing green roofs amount, and decrease from 2.86% to 2.01% with the increasing return period of rainfall events. The catchment of the Zhongshan Road business district in the southern city core area plays a key role in reducing runoff, by 8.84% under the two-year return period of rainfall events and 100% green roofs implementation scenarios. (2) The areas prone to stagnant water on Xiamen Island are mainly distributed in Gaoqi Airport, the northwest port, Yundang Lake, Wuyuan Bay, and Huandao Road. The average ponding depth decreased by 1.68, 4.68, 6.45, 14.43 cm and the ponding area decreased by 6.11, 16.89, 23.29, 52.06 hm² under the four green roofs scenarios. The reduction rate of the ponding area decreases with the increasing rainfall return period. Green roofs have a significant effect on ponding mitigation under low to moderate intensity rainfall. The study demonstrated the positively hydrological performance contributed by green roofs in the future Xiamen Island at a city scale, and could effectively respond to the water security problems of highly urbanization. In addition, analysis of spatial heterogeneity characteristics of hydrological performance of green roofs can provide scientific guidance for urban ecological governance. Zhongshan Road should take green roofs as a key ecological strategy to mitigate pond; the northwest port should consider other broader ecological strategies; Gaoqi Airport should include roof greening as a mandatory content of the unified development plan after relocation. In addition, this study is carried out under the background of coastal cities with subtropical monsoon climate. The results may not be applicable to other climatic conditions and different types of green roofs, but it will be of reference significance for similar comparative studies.