Abstract This paper presents a study on mitigating the degradation of ballast by placing an under-sleeper rubber pad (USP) beneath a sleeper. Large-scale track process simulation apparatus (TPSA) tests have been carried out on ballast assemblies (with and without USP) subjected to cyclic loadings. Numerical modelling has been performed using a coupled discrete-continuum modelling (coupled DEM-FDM) approach to investigate the role of USP from a micromechanical perspective. Ballast grains are simulated in DEM by bonding of many cylinders together at appropriate sizes and locations; and when those bonds break, they are considered to represent ballast breakage. The capping and subgrade layers are simulated as continuum media using the finite difference method (FDM). Interface elements were developed for transmitting forces and displacements between the discrete and continuum domains. The coupled model is validated by comparing the predicted load-deformation responses with those measured from large-scale TPSA tests. The model is then used to explore changes in the micromechanical aspects of ballast subjected to cyclic loading, including particle connectivity number, contact force distributions, and contact orientations and associated particle breakage. These findings are needed to gain a better insight as to how USPs help to attenuate the load applied in a ballast assembly.