The demand for analysis of large‐scale data has increased with increased access to spatial vector data. Polygon overlay of vector data in a virtual globe requires proprietary data structures and proprietary analysis algorithms. A vector data structure is designed for rapid polygon overlay in a virtual globe by recording the metadata of the triangles (TriMeta) that constitute polygons. A polygon overlay algorithm is proposed based on this data structure. The overlay of two complex GIS polygons is transformed into the intersection computation of their 3D triangular presentations. The intersection computation of two sets of triangles is reduced considerably by utilizing TriMeta to filter out the disjoint triangle pairs and rapidly identify the contained triangle. The new method improves the overlay efficiency in a virtual globe because the amount of computation required to calculate the intersections of two large polygons and drape the intersections onto a terrain surface is reduced.