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Abstract Optical manipulation of coherent phonon frequency in two-dimensional (2D) materials could advance the development of ultrafast phononics in atomic-thin platforms. However, conventional approaches for such control are limited to doping, strain, structural or thermal engineering. Here, we report the experimental observation of strong laser-polarization control of coherent phonon frequency through time-resolved pump-probe spectroscopic study of van der Waals (vdW) materials Fe 3 GeTe 2 . When the polarization of the pumping laser with tilted incidence is swept between in-plane and out-of-plane orientations, the frequencies of excited phonons can be monotonically tuned by as large as 3% (~100 GHz). Our first-principles calculations suggest the strong planar and vertical inter-atomic interaction asymmetry in layered materials accounts for the observed polarization-dependent phonon frequencies, as in-plane/out-of-plane polarization modifies the restoring force of the lattice vibration differently. Our work provides insightful understanding of the coherent phonon dynamics in layered vdW materials and opens up new avenues to optically manipulating coherent phonons.