The electron-phonon coupling (EPC) in a material is at the frontier of the fundamental research, underlying many quantum behaviors. van der Waals heterostructures (vdWHs) provide an ideal platform to reveal the intrinsic interaction between their electrons and phonons. In particular, the flexible van der Waals stacking of different atomic crystals leads to multiple opportunities to engineer the interlayer phonon modes for EPC. Here, in hBN/WS2 vdWH, we report the strong cross-dimensional coupling between the layer-breathing phonons well extended over tens to hundreds of layer thick vdWH and the electrons localized within the few-layer WS2 constituent. The strength of such cross-dimensional EPC can be well reproduced by a microscopic picture through the mediation by the interfacial coupling and also the interlayer bond polarizability model in vdWHs. The study on cross-dimensional EPC paves the way to manipulate the interaction between electrons and phonons in various vdWHs by interfacial engineering for possible interesting physical phenomena.