To investigate the influence of the structural deformation of the wheelset and track on rail wear in the longitudinal and lateral directions, a rail wear prediction model is established that can calculate the three-dimensional distribution of rail wear. The difference between the multi-rigid-body dynamic model and the rigid-flexible coupled dynamic model, which considers the structural flexibility of the wheelset and track, is compared in terms of the three-dimensional distribution of rail wear. The results show that the three-dimensional distributions of rail wear predicted by the two models are relatively similar. There is no obvious difference in the wear band, and the rail wear in the longitudinal direction is almost identical. The cross sections of the worn rail shapes determined by the two models are essentially the same, with a maximum difference of 3.6% in the average value of the wear areas of all cross sections. The track irregularity is the main reason for the uneven distribution of rail wear in the longitudinal direction. The position where the rail wear is more pronounced hardly varies with the evolution of the rail wear. It is recommended to use a multi-rigid-body dynamic model for the prediction of rail wear, which allows both calculation accuracy and efficiency.