The under-sleeper pad (USP) is extensively used in railway track structures due to its desired damping performance. The impact of USP on the stiffness and dynamic responses of track structures was well documented in the majority of the existing studies; however, few studies focus on its influence on the lateral resistance of the ballast bed. To address this deficiency and further disclose its governing mechanisms, a refined DEM-FDM numerical model was established for the three-dimensional (3D) sleeper-USP-ballast bed-subgrade system. The numerical model was subsequently calibrated and verified by using field-measured lateral resistance results of a typical heavy-haul railroad. The influencing mechanisms of USP on the multiscale performance indicators including lateral resistance of different parts of the loaded sleeper, ballast particle motion, and contact force were disclosed from a variety of numerical simulation scenarios. The results show that at the same level of lateral displacement, the mobilized ballast particles under the sleeper with USP had a deeper range of motion than those under the sleeper without USP, which led to greater lateral resistance. The unevenness of the USP surface is a major contributing factor to the increase in lateral resistance. Greater USP stiffness results in higher lateral resistance. The use of the USP could increase the lateral shear stress and the maximum normal contact forces under the sleeper, both of which increase with increasing USP stiffness.