Abstract: Topological overlay analysis of vector polygons is the key and fundamental spatial analysis method to extract spatial implicit information. The existing methods are mainly for the simple data structure, not taking into account the spatial relationship of map elements and the composite operation between them. In order to implement the topology overlay for vector polygon maps in the mode of spatial operation favor- ing spatial relationship composition, we presented a new topology overlay algorithm based on arc and poly- gon operation in this paper. The algorithm, for the two vector polygon maps to participate in topology over- lay, carries out respectively the overlay operators and spatial relationship composition for the every vector arcs of one and polygonal area map of another. In this process those arcs crossing polygon unit can be de- tected and decomposed, finally the result polygon map with spatial topological relationship has been gener- ated by overlay mode oriented arcs filtering, nodes matching, and spatial relationship reconstruction. The computational experiment shows that the proposed algorithm has higher robustness and efficiency, which is very suitable for spatial topological overlay analysis of complex polygon maps with spatial relationship.