The impervious area on the surface of urban area has been increased as buildings and artificial land cover have continually been increased. Urban development has gradually decreased the green zone in downtown and alienated the city from the natural environment on outskirt area devastating the natural ecosystem. There arise the environmental problems to urban area including urban heat island phenomenon, urban flood, air pollution and urban desertification. As one of urban plans to solve such problems, green roof system is attracting attentions. The purpose of this study was to investigate flood discharge and heat reduction effect according to the green roof system and to quantify effect by analyzing through simulation water and heat cycle before and after green roof system. For the analysis, Distributed hydrologic model, WEP (Water and Energy transfer Processes) and WEP+ model were used. WEP was developed by Dr. Jia, the Public Works Research Institute in Japan (Jia et al., 2005), which can simulate water and heat cycle of an urban area with complex land uses including calculation of spatial and temporal distributions of water and heat cycle components. The WEP+ is a visualization and analysis system for the WEP model developed by Korea Institute of Construction Technology (KICT).