A watershed is not only a complete natural geographical unit, with a defined ecological and hydrological pattern, but is also an area with concentrated human activity. Because of these features, it is widely recognized as the optimal scale to analyze ecological environments. However, one of the problems that arise when analyzing data at the watershed scale is how to store and manage the necessarily large data sets, specifically through database design and implementation. In China, there has been a lack of database design and application for multi-source, multi-scale, cross-band environmental data. Theory of the integrative spatial and attribute data, the "3S" (geographic information system; remote sensing and global positioning system), a spatial data engine (SDE) and spatial data warehouse techniques were used to build a large environmental database to analyze the present situation and the future requirements of the Tarim River Basin. In this paper, several important issues are discussed including methods for seamless integration of multi-source data, database specification design, element coding design, spatial index design, characteristic display table design, and input with one key design, among others. Initially, the physical data layer and logical data layer are separated, followed by the vector data and the raster data, and data is fully integrated in a unified multi-scale space frame system for the crack problems after cross-band operation in the Tarim River Basin. Database specification design, particularly the database naming convention, is an important part of data design and storage. Based on the relevant principles, and standards, the names of six categories of data sources, metadata and index graph were standardized by English abbreviations to improve user access of the large database. Element coding design aims to provide a unified correspondence for data storage, query, and analysis. Element coding design standards can be established according to the scales of graphics data, which is the basis for information sharing. Spatial index design is a key determinant of the efficiency of database access. The use of ArcSDE to provide a spatial index of vector data and the construction of a multi-level pyramid structure for raster data can improve the efficiency of data search. The characteristic display table is based on a data dictionary and meta table, mainly for its system information display service. By constructing the characteristic display table, the corresponding code is only called by the system when it is needed, which greatly improves the efficiency of display and response. Input with one key is proposed to solve problems associated with ineffective data storage and complicated operations, and to promote the reliability of data storage. Collectively, the above steps help achieve seamless integration and unified management of multi-source, multi-type, and large scale eco-environmental data collected at the watershed scale, which can offer possible data support for dynamic monitoring of the environment. The theory and practical application of this study can be extended to other basins or other database types.