The penetration of ballast in ballast track significantly affects subgrade performance. A unit specimen was designed with ballast on top and subgrade soil below. Laboratory dynamic triaxial tests and discrete element method (DEM) simulations were used to study the macroscopic deformation behavior and local deformation characteristics of crushed ballast penetration into soil subgrade under dynamic loads. The results indicate that, under train-induced dynamic loads, the ballast and subgrade soil only transmit stress through a limited number of discrete contacts at the interface. As the dynamic stress amplitude increases, the depth of ballast penetration into subgrade soil also increases, exhibiting an exponential relationship with the dynamic stress. The deformation process of the ballast penetration specimens can be divided into three stages: localized compression, shear band formation, and shear band development. Under train-induced loads, ballast penetration significantly increases the porosity of soil samples near the ballast-subgrade interface, and causes significant lateral deformation at the contact interface. Saturated specimens with higher porosity can experience mud pumping under relatively low dynamic stress. The increase in subgrade surface porosity caused by ballast penetration is a significant factor contributing to mud pumping in existing railways. Prevention of mud pumping should focus on preventing the local increase in subgrade porosity caused by ballast penetration. The findings deepen our understanding of the ballast penetration phenomenon and the resulting deformation behavior of the subgrade surface.