Green roof is an important facility to mitigate urban flood resulted by increasing urbanization and impermeable surface. A thick substrate material layer with plants, grass, and/or trees, and extra structural support is one of main components of green roof. Due to the complexity of rainwater storage mechanism in the substrate material layer, the simulations results on rainfall-runoff on green roof are mostly unsatisfactory. In this study, the runoff reduction effect of green roof was simulated by considering the effect of substrate material layer on runoff. The green roof was compared with slope roof, plane roof and retention roof in order to understand the effect of substrate material layer on runoff. The experiment was carried out in Beijing Water Science and Technology Institute, China. The precipitation was measured by using a self-recording tipping bucket rain gauge. Runoff was monitored by using an equipment including water level gauges and triangular weir. The runoff coefficient and rainwater retention rate were calculated. A total of 11 rainfall-runoff events were monitored in 2015. The results showed that the change of the runoff coefficient was highly complex and it was influenced by many factors, e.g., precipitation, average/maximum rainfall intensity, and interval time between rainfall events. For all the monitored rainfall events, the average runoff coefficient values for plane roof, slope roof, green roof and retention roof were 0.68, 0.84, 0.41 and 0.43, respectively. The average rainwater retention rate values of green roof and retention roof were 58.9% and 57.2%, respectively. It indicated that the runoff reduction effects of green roof and retention roof are similar but both were better than the other two types of roofs. The runoff process of green roof was also similar with that of retention roof under the same rainfall conditions. Both the outflow processes from green roof and retention roof could be regarded as an unsteady orifice flow under the effect of accumulated water head on the roof-top. Thus, a unit hydrograph model to simulate runoff from green roof was proposed based on the saturated infiltration theory that included the thickness limitation of the substrate material layer and the influence of water accumulated on the surface. By using the proposed unit hydrograph model, the rainfall-runoff processes on green roof were simulated. The simulation results showed that the trends of the simulated and measured runoff were consistent well. The coefficient of determination and Nash-Sutcliffe efficiency were 0.85 and 0.84, respectively. This study will be helpful for further understanding the runoff reduction effect and the outflow mechanism of green roofs.