This paper deals with electronic map data index based on Embedded Linux System, and introduces the basic ways about spatial index. By analyzing the common indexed algorithms, such as B Tree, B+Tree, R Tree, Quadtree and so on, it designs the spatial data indexed structure based on Hilbert grid and modifies the data structure. Index eficiency is improved because of the modified structure. Finally, it uses the SQLite database to manage the spatial data and achieves expected effect.