The combination of non-trivial band topology and symmetry breaking phases gives rise to novel quantum states and phenomena such as topological superconductivity, quantum anomalous Hall effect and axion electrodynamics. Evidence of intertwined charge density wave (CDW) and superconducting order parameters has recently been observed in a novel kagome material AV3Sb5 (A=K,Rb,Cs) that features a Z2 topological invariant in the electronic structure. However, the origin of the CDW and its intricate interplay with topological state has yet to be determined. Here, using hard x-ray scattering, we demonstrate a three-dimensional (3D) CDW with 2*2*2 superstructure in (Rb,Cs)V3Sb5. Unexpectedly, we find that the CDW fails to induce acoustic phonon anomalies at the CDW wavevector but yields a novel Raman mode which quickly damps into a broad continuum below the CDW transition temperature. Our observations exclude strong electron-phonon coupling driven CDW in AV3Sb5 and point to an unconventional and electronic-driven mechanism that couples the CDW and the topological band structure.