In desert regions, sand intrusion into the ballast bed is unavoidable, leading to a reduction in the elasticity of the ballast bed and posing potential risks to the service safety. Previous studies have focused on the behaviors of sandy ballast beds in 2D planes using discrete element method (DEM), where sand content is typically calculated utilizing sand areas within the ballast voids, different from that using sand volumes or mass in 3D space. Therefore, the impacts of sand content on the multiscale responses of the ballast bed are not fully addressed. In this paper, 3D full-scale half-sleeper models with various sand contents are established via DEM. Multiscale responses of sandy ballast bed obtained by laboratory tests are utilized to verify the reliability of established models. Simulation results show that macroscopically, sand intrusion increases the stiffness and consequently reduces the elasticity of the ballast bed. Microscopically, sand contaminant restricts the translational acceleration of ballast particles, while simultaneously intensifying the angular acceleration. In terms of particle contact, the anisotropy of the directional distribution of contact force among ballast particles is weakened by sand contaminant. Therefore, the inter-particle contact force among ballast particles becomes more uniform, particularly beneath the rail. A normalized parameter is proposed to quantify the filling effect of sand contaminant, based on which the relationships between multiscale dynamic responses and sand content are linearized. The linearization results indicate that the sand intrusion has more significant impacts on the multiscale responses of the ballast bed under higher loading magnitude.