The online transmission and real‐time rendering of complex 3D models have always been a bottleneck which limits the performance of Web 3D simulation systems. To improve the efficiency of data transmission and mesh reconstruction, this article proposes a novel progressive mesh structure. In the first stage of progressive visualization, the base data and the base index generated by vertex clustering simplification are transmitted to the client for the fundamental rendering. Then the incremental data and corresponding indexes at higher levels are transmitted, as the viewpoint approaches the simulation object. The multi‐scale incremental data organization benefits the performance and efficiency of the Web 3D simulation system by separately transmitting and reconstructing the corresponding level of mesh details. To demonstrate the adaptability and reliability of this algorithm, we developed an experimental prototype system to conduct a series of experiments. The results of experiments show that the improved progressive mesh structure described in this article takes good advantage of the vertex clustering simplification scheme to increase the efficiency of online transmission and mesh reconstruction, and the average frame rate of the progressive visualization has been increased to some extent, especially for massive data in large scale scenes.