A coupling dynamic model of a subway train and an embedded track is established to study the safety limits of track irregularities. The simulated vehicle system was a 74-degrees of freedom multi-rigid body model, and the rail was a Timoshenko beam. The slab was a three-dimensional solid finite element model. The sensitive wavelength irregularity was first studied, and then the safety limit of the sensitive wavelength was analyzed. The wheel-rail lateral force exhibited a substantial effect on the track alignment and gauge irregularity safety limit. The wheel-rail vertical force and the rate of wheel load reduction significantly affected the height and cross-level irregularity safety limit. The results demonstrate that the safety limits of the alignment, gauge, height, and cross-level embedded track geometric irregularity are 5.3 mm, [− 10.5, 8] mm, 5.6 mm, and 6 mm, respectively.