During the mechanical cleaning operation on ballast bed， backfilling ballast in batches would lead to a layered and uneven ballast distribution. To reveal the effect of uneven ballast distribution on the mechanical properties， the simulation model of ballast bed was generated based on the basic principle of discrete element method. Then three kinds of ballast layering distributed conditions were simulated in the model， the uniform distribution， "large upper and small lower" distribution and "small upper and large lower" distribution， respectively. And the mechanical characteristics of ballast bed during the tamping operation and the stabilizing operation were analyzed. The results show that the uneven ballast distribution has impact on the mechanical properties of ballast bed. The compactness of ballast bed is less affected， while the vertical stiffness and the lateral resistance are obviously affected. During the tamping operation， the "small upper and large lower" ballast distribution is most conducive to improve the vertical stiffness. While during the stabilizing operation， the "large upper and small lower" ballast distribution is most conducive to improve the transverse resistance. The flow of ballast particles is an important factor to improve the vertical stiffness and the lateral resistance of ballast bed.