With the development of information technology, spatial data plays an increasingly important part in both people’s daily life and industrial manufacture. The demand of spatial data processing and retrieving is challenging traditional database technology. The emergence of spatial database has greatly raised the efficiency of spatial data handling. As the key component of spatial database, spatial index technology got a booming development in the past few years; kinds of new index structure is being developed, improved, and eliminated. This article pays attention to the spatial index structure; we first give a survey on the mesh index structure, present the classical R-tree index structure and its variations, then according to the nature of GIS data, we develop a new spatial index structure for GIS data composing the advantage of mesh index and R-tree index, and verify its high efficiency experimentally.