In order to investigate the uneven settlement of bridge-embankment transition section, a full-scale three-dimensional transition zone model has been proposed, which utilizes a coupling approach involving the Discrete Element Method (DEM) and Multibody Dynamics (MBD). The coupled DEM-MBD model was developed to analyze the behavior of wedge-shape backfill treatment from macro and micro views. M-wave loading pattern was applied, and the accuracy of this comprehensive model was validated by replicating uneven settlement patterns under train loading. Simulation results show that the wedge backfill reinforcement significantly inhibits sleeper settlement, with the maximum settlement of sleepers in the transition subgrade area decreasing from 2.04 mm to 1.38 mm, a reduction of 32.1%. The uneven settlement in the transition section decreases from 1.51 mm to 0.92 mm, a reduction of 39.1%. Furthermore, the use of wedge backfill increases the number of ballast particles transmitting contact forces beneath sleepers. The contact force chains in the ballast layer disperse with a larger angle, effectively strengthening the support of the track bed. Simultaneously, the particle velocity beneath the sleepers decreases significantly with wedge backfill, restraining particle motion, and thereby reducing sleeper settlement at a macro level.