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Phonons are important lattice vibrations that affect the thermal, electronic, and optical properties of materials. In this work, we studied infrared phonon resonance in a prototype van der Waals (vdW) material—hexagonal boron nitride (hBN)—with the thickness ranging from monolayers to bulk, especially on ultra-thin crystals with atomic layers smaller than 20. Our combined experimental and modeling results show a systematic increase in the intensity of in-plane phonon resonance at the increasing number of layers in hBN, with a sensitivity down to one atomic layer. While the thickness-dependence of the phonon resonance reveals the antenna nature of our nanoscope, the linear thickness-scaling of the phonon polariton wavelength indicates the preservation of electromagnetic hyperbolicity in ultra-thin hBN layers. Our conclusions should be generic for fundamental resonances in vdW materials and heterostructures where the number of constituent layers can be conveniently controlled. The thickness-dependent phonon resonance and phonon polaritons revealed in our work also suggest vdW engineering opportunities for desired thermal and nanophotonic functionalities.