In the analysis of applying high order Discontinuous Deformation Analysis (DDA) to continuous structures, some stiff junction pairs are required to be set on the adjacent faces between blocks to connect the discrete blocks into a whole. Nonetheless, it involves great difficulty to rapidly lay out these points  for complex structures with multiple structural members. In this paper, the geometric method algorithm to generate Voronoi tessellation is improved on the basis of Voronoi tessellation theory, and the locations of the points are optimized with centroid method. Program is compiled based on the above optimizations and is verified by several examples. The calculation results show that a series of points well distributed in an arbitrary convex polygon can be generated quickly with the suggested method, which thus could be applied in three-dimensional high order DDA analysis easily.