To investigate the influences of through-transverse mortar disengagement with different lengths and heights on the dynamic responses of vehicle and track systems under the high frequency train loads, a coupled rigid vehicle–flexible track multi-body dynamics (MBD) model with mortar disengagement was established in SIMPACK platforms with the help of ANSYS software. The results indicate that when the mortar disengagement length is no more than 1 m, the responses of vehicle and track systems are hardly influenced by mortar disengagement with an increase rate of no more than 10% except for the slab displacement. When LMD reaches 1.5 m, the maximum slab displacement exceeds the safety limit of 0.5 mm. The vertical wheel–rail contact force and the rail displacement exceed the safety limit with the mortar disengagement length of 2 m and the mortar disengagement height of 1.5 mm. The most increase rates induced by mortar disengagement are 190% and 272% with regards to the slab displacement and the longitudinal tension stress of slab, respectively, which is significantly detrimental to the service life of slab. The proposed approach has the potential to preliminarily determine the critical mortar disengagement size, which is conductive to relieving the pressure of track maintenance while ensuring the service life of track structures and the operation safety and riding comfort of the vehicle.