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Aiming at multi-scale representation of spatial data not supported by R-tree and the objects in the same rank are not-clustered, a multi-scale index structure of spatial data based on cluster algorithm is proposed. Hierarchical structure of index tree is made use of reflecting the change of resolution ratio. The spatial objects of the same rank are divided into different groups using k-means cluster algorithm, decreasing the region covering and region overlap. The result of our experiments shows that the algorithm, compared with other ways, has a distinct superiority in the speed of multi-scale display of spatial data.