Abstract: In this study, the traditional Voronoi diagram method was improved, and the microstructure model of columnar crystals and fine and coarse equiaxed mixed crystal structure of the weld zone was established to study the fatigue crack initiation process of micro-scale weld joints. Firstly, the weld zone was divided into different microscopic zone according to the results of metallographic experiments. Then the microstructure model of the mixed crystal zone was created by controlling the density and position of the seed points in different micro zones. Finally, the microstructure model of the integral weld zone was merged by Boolean operation. The results show that the microstructure model of the weld joint established by this method has a high similarity with the real structure. The model is applied to the simulation of the fatigue crack initiation process of the GH4169 electron beam welded joint, which show good agreement with the experimental results.