Focusing on the issue that there exist defects of vertex data redundancy and lack of adjacency information among the faces in the STereo Lithography (STL) file format, an explicit algorithm of surface topology reconstruction was presented based on the multi-dimensional dynamic spatial index. During the process of eliminating the copies of the mesh vertex data, the K-Dimensional Tree (KD Tree) of the vertices on the mesh surface was gradually built. The efficiency of eliminating the vertex copies was improved by the index and the surface topology was rapidly built based on the storage openness of the data in the leaf node layer of KD-tree, in which the half-edge data structure could be integrated. Finally, compared with methods using R ^*-Tree, array and hash table as index, the proposed dynamic spatial index integrated KD-Tree with half-edge date structure used 11.93 s to remove redundant vertices and 2.87 s to reconstruct surface topology when dealing with the data file of nearly one million faces, which significantly reduced the time of eliminating the redundant vertices and surface topology reconstruction. And the index effectively supported quick query of the topology information of mesh surface with the query time in 1 ms, which was far less than the comparison algorithms. The experimental results show that the proposed algorithm can improve the efficiency of eliminating the vertex data redundancy and the topological reconstruction as well as achieve quick query of the topology information of mesh surface.