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Using spatial database, geographic information system (GIS) technology and system engineering theory, the hydro-ecological spatial database was built, and the corresponding hydro-ecological spatial database management information system was designed and developed. From aspects of the data organization and classification, the overall structure of the database, database construction processes and data integration methods, the design and key technologies of hydro-ecological spatial database were elaborated and discussed. And combining with this database, the hydrological database management system based on ArcGIS Engine was developed. The functions of management, storage, query, analysis were realized in the system. The system provided a integrated data processing platform for the security evaluation and prediction of hydro-ecological system in arid areas, effectively improved efficiency of the mass data storage, management, processing and spatial analysis capabilities, as well as increased the work efficiency.