Scenario modeling and risk assessment of natural disaster is one of the hotspots of disaster research. However, urban natural disaster risk assessment, so far, is lack of common procedures and program. This paper selects rainstorm water-logging as research disaster, which is one of the most frequent occurring hazards in most cities of China, and sets up a small-scale based integrated methodology for hazards risk assessment of rainstorm water-logging, taking Jing'an District in Shanghai as an example. Based on the basic concept of disaster risk, this paper applies scenario modeling to express the risk of the small-scale urban rainstorm water-logging disasters in different return periods. Through the analysis of hazards, vulnerability and exposure, we simulate different disaster scenarios and propose a comprehensive analysis method and procedure for the small-scale urban storm water-logging disaster risk assessment. A grid-based GIS approach, including urban terrain model, urban rainfall model, urban rainfall model and urban drainage model, was applied to simulate inundation area and depth. And then, stage-damage curves for residential buildings and contents were generated by the loss data of water-logging from the field surveys and the insurance company, which were further applied to analyze the vulnerability, exposure and loss assessment. Finally, the exceedance probability curve for disaster damage was constructed by using the damages of each simulated event and its respective exceedance probabilities. A framework was also developed for coupling the water-logging risk with the risk planning and management through exceedance probability curve and annual average of water-logging loss. And this is a new exploration for small-scale urban natural disaster scenario simulation and risk assessment.