In railway tracks, ballasted track beds, consisting of assemblies of crushed stone particles, are widely used to distribute train loads, mitigate wheel-rail impact forces, and ensure adequate drainage performance. However, under repeated train loading, ballasted track beds undergo irreversible deformation, which leads to track deterioration such as ballast settlement. This irreversible deformation of ballast is particularly significant at ballast-concrete slab transition zones and at rail joints. In such regions, dynamic vehicle-track interactions amplify the external forces acting on the ballasted track bed, which are manifested macroscopically as ballast settlement and track deterioration. In this study, we present an FE-based simulation method that couples wheel-track vibration analysis with the cyclic deformation analysis of ballasted track beds. Track vibration analysis is performed to predict the maximum forces acting on each rail pad during train passage. The rails and sleepers are modeled as frame elements or lumped masses. The rail pads are represented by Voigt units. This vibration model can also account for rail irregularities, complex contact conditions at rail joints, and hanging sleepers. In the ballast cyclic deformation analysis, the irreversible deformation of ballast is simulated using an elastoplastic finite element method incorporating the cyclic densification model proposed by Suiker and de Borst. This elastoplastic model consists of a monotonic loading process based on a modified Drucker-Prager yield surface with a non-associative flow rule, and a cyclic loading process formulated using Perzyna's overstress concept. In the cyclic loading analysis, the maximum force acting on each rail pad obtained from the vibration analysis is applied as the external load in the elastoplastic FE analysis. The proposed coupled simulation method is employed to investigate the effects of shape dimensions and material parameters of track components on the suppression of ballast settlement at rail joints. In particular, the use of under-sleeper pads (USPs) and grid-shaped sleepers is shown to be effective.