With the development of urbanization, urban nonpoint source pollution has become the main reason for deterioration of water quality in receiving water body. Green roof is one of the important technologies for controlling urban nonpoint source pollution, which has been taken as an important component of technical system in many advanced concepts for the management of urban stormwater runoff. Green roofs not only provide many general environmental and associated aesthetic, but also play an important role in increasing the green space in densely populated urban areas. So, with increasing of research interests in vegetated roof, more and more such installations are being built in urban regions. However, the water quality of runoff from green roof has been paid little attention so far, and always been consumed clean. Results from recent studies show that green roofs always become source of some pollutants, especially nitrogen and phosphor. The water quality of green roof runoff can be influenced by many factors, such as green roof media, plants vegetated, rainfall intensity, and so on. As long as the water quality issues remain outside the design phase, there is a large potential for green roofs to become pollution sources. So, it is very important to investigate runoff water quality from green roofs under different environment and installation methods. In this paper, in order to investigate the concentrations distribution and composition of nitrogen and phosphor in stormwater runoff from green roofs, two types of green roofs were constructed in Chongqing University and the water quality of storm runoff from them and the reference roof were monitored from September 2009 to October 2011. Results show that green roofs can improve pH of rainwater from 5.5 to 7.7, which indicates the rapid neutralization for the acid depositions and an environmental benefit in case roof runoff is directly discharged to natural water recipients. The concentrations of NH₃-N in runoff from green roof are lower than the value as requested in standard Ⅲ of Environmental Quality Standards for Surface Water, so, nitrification occurs when rainwater flows through green roofs. The mean concentrations of TN, TP and NO₃^--N in storm runoff are 3.6-4.4mg/L, 0.17-0.28 mg/L and 3.1-3.7mg/L respectively, which are higher than that in rain water. Compared with the water quality of contemporaneous stormwater runoff from reference roof, the concentrations of TN, NH₃-N and TP in runoff from green roofs are lower relatively, while the concentrations of NO₃^--N and PO₄^3--P are higher. The water quality of stormwater runoff from green roofs varies significantly with seasons, which is better in summer and worse in spring and autumn. Overall, the concentrations of TN and NO₃^--N in runoff from green roofs decrease gradually when they are operated for long term, while that of TP and PO₄^3--P shows fluctuations. Analysis of Pearson correlations among meteorological factors indicates that the higher temperature and longer drying period, the more decrease of concentration of NH₃-N. The TP and NH₃-N of runoff in green roofs come from rain water primarily. This study can give an important reference for the construction of green roofs and the management of urban stormwater runoff.