The Inner Mongolia Autonomous Region is facing the dual threat of drought, semi arid and regional water source environmental safety for a long time. Moreover, the technology for environmental safety management is seriously outdated. In this paper, we have established the basic database of the surface morphology, hydrology, water quality, pollution sources, fracture surface and spatial water source environmental information in the Inner Mongolia Autonomous Region. In consideration of the strong spatial characteristics of the water source environmental information, the Inner Mongolia Autonomous Region water environmental safety management information system is developed on the ArcGIS network platform with C++ language and B/S architecturein this paper. The system not only achieves the visual computer management of the spatial information of water source but also provides guidance for the division of water source and water source protection management combining with water source and environmental monitoring, pollution sources and other data for the environmental safety analysis. Using the developed method in some cities of Inner Mongolia, the system shows strong practicability, information display intuitive and good universality, which provides effective decision support for environmental safety, high efficiency management and early warning of the water source in the autonomous region.