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GIS as the platform is being widely used in current construction of geoscience spatial database in China, and the quality of its spatial data directly influences the quality of the spatial database of geoscience. Precision of spatial data, validity and integrality of attribute data, and validity of the spatial database's topological relations are the main factors which influence the quality of the spatial database. Through practical summarize, the article discusses concrete means and methods to control the data quality of the three aspects mentioned above. By the means and methods, the data quality can be guaranteed to meet the needs for setting up spatial database of geoscience and building up a spatial database of geoscience with good quality.