To better constrain the deep structure and dynamics of the Western Alps, we studied the mantle transition zone (MTZ) structure using P-wave receiver functions (RFs). We obtained a total of 24904 RFs from 1182 events collected by 307 stations in the Western Alps. To illustrate the influence of the heterogeneity on the upper mantle velocity, we used both IASP91 and three-dimensional (3-D) velocity models to perform RF time-to-depth migration. We documented an MTZ thickening of about 40 km under the Western Alps and most of the Po Plain due to the uplift associated with the 410-km discontinuity and the depression associated with the 660-km discontinuity. Based upon the close spatial connection between the thickened MTZ and the location of the subducted slabs, we proposed that the thick MTZ was due to the subduction of the Alpine slab through the upper MTZ and the presence of remnants of subducted oceanic lithosphere in the MTZ. The uplift associated with the 410-km discontinuity provided independent evidence of the subduction depth of the Western Alps slab. In the Alpine foreland in eastern France, we observed localized arc-shaped thinning of the MTZ caused by a 12 km depression of the 410-km discontinuity, which has not been previously reported. This depression indicated a temperature increase of 120 K in the upper MTZ, and we proposed that it was caused by a small-scale mantle upwelling. Hardly any uplift of the 660 km discontinuity was observed, suggesting that the thermal anomaly was unlikely to be the result of a mantle plume. We observed that the thinning area of the MTZ corresponded to the area with the highest uplift rate in the Western Alps, which may have indicated that the temperature increase caused by the mantle upwelling contributed to the topographic uplift.