In order to discuss the influence of different track structures on the structure-borne noise of an elevated concrete box-girder, the theoretical analysis model of vehicle-track coupling system and the statistical energy model of bridge noise were established considering the influence of multiple wheels. Based on the on-site noise test of a 30m concrete simple box-girder on a rail transit line, the simulation model was validated. Then, the influence laws of the force applied on the box-girder, the input power and associated noise of the box-girder were discussed for three kinds of track structures (i.e., embedded sleepers, trapezoidal sleeper and steel spring floating slab). The research results show that the simulated values are in good agreement with the measured ones, indicating the structure-borne noise of the box-girder can be well predicted. The input power of the box-girder and the power of subsystems depend on the force applied on the box-girder. The frequency variation of the field noise is mainly affected by the input power of the box-girder. The type of track structure has a great influence on the noise radiated from the box-girder. With respect to the overall sound level, the embedded sleeper case is the largest, the trapezoidal sleeper case takes the second place, and the steel spring floating slab case is the smallest.