Particle shape plays an essential role in deformation characteristics of railway ballast bed. The numerical reconstruction of ballast morphological features, including overall shape and angular distribution, remains a hot issue in research on ballast mechanical behavior simulation. A novel shape reconstruction method was adopted to generate ballast particles that met the desired probability density distribution of morphological indices. On this basis, the numerical model of ballast triaxial tests were established under different confining pressures. The results were compared with those obtained from indoor tests and simulations whose particles were generated from 3D scanning or non-statistical random generation. The results show that the particle shape has a growing effect on the mechanical response of ballast, with an increase in confining pressure. The relation between deviatoric stress and axial strain in the specimen which meets the probability density distribution is more consistent with the experimental results than that of the non-statistical randomly generated specimen. The lateral deformation of ballast is correlated with the adjustment of the packing structure. For non-statistical randomly generated specimen, both the lateral deformation and the particle adjustment are larger than those generated by 3D scanning. The ballast contact force evolution is less influenced by its morphological features. Nevertheless, the difference in the maximum contact force of specimens with various particle shapes is nearly 50%.