The short fatigue crack initiation of LZ50 axle steel for railway vehicles was investigated by numerical simulation in this paper. The microstructure of LZ50 steel was constructed with the application of 2D Voronoi tessellation. The stress and strain distributions in the microstructure were obtained by FEM under the boundary condition shifted from loading level applied in fatigue specimen of this steel. Finally, the probability of short fatigue crack initiation was given with different loading cycles to illustrate the process of crack initiation of LZ50 steel under the given loading cycles based on the S-N curve of the material. The further work on the research of crack growth and collective evolution of short fatigue cracks can be conducted with the simulated results of crack initiation in the microstructure of LZ50 steel.