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Urban natural disaster risk research is one of the effective ways on urban regional implementation of risk reduction and mitigation strategies. Disaster risk assessment and zoning is the frontier and hot issue in international disaster risk field. Geographic Information System (GIS) technology is an important aiding tool for natural disaster risk researches. Over the past five years, we studied the integrated toolkit for urban natural disaster risk research supported by Shanghai Youth Science and Technology Venus Program (09QA1401800) `Natural disaster risk assessment and zoning in Shanghai based on the scenarios simulation technology' and National Science Key Foundation in China (40730526) `Study on natural disaster contingency planning for China's coastal cities based on risk scenario analysis'. The integrated toolkit system was designed and developed based on ArcEngine 9.3 components technology, NET Framework development environment, and C# language, it includes five functional modules: (1) evolution analysis of hazard-formative environments, (2) hazard analysis of disaster-making factors, (3) vulnerability assessment of hazard-affected bodies, (4) disaster loss assessment and risk zoning, and (5) simulation of disaster emergency shelter. The integrated toolkit can be used by the government to establish urban natural disaster mitigation strategies.