The Kitaev quantum spin liquid epitomizes an entangled topological state, for which two flavors of fractionalized low-energy excitations are predicted: the itinerant Majorana fermion and the Z2 gauge flux. Detection of these excitations remains challenging, because of their fractional quantum numbers and non-locality. It was proposed recently that fingerprints of fractional excitations are encoded in the phonon spectra of Kitaev quantum spin liquids through a novel fractional-excitation-phonon coupling. Here, we uncover this effect in $alpha$-RuCl3 using inelastic X-ray scattering with meV resolution. At high temperature, we discover interlaced optical phonons intercepting a transverse acoustic phonon between 3 and 7 meV. Upon decreasing temperature, the optical phonons display a large intensity enhancement near the Kitaev energy, JK~8 meV, that coincides with a giant acoustic phonon softening near the Z2 gauge flux energy scale. This fractional excitation induced phonon anomalies uncover the key ingredient of the quantum thermal Hall effect in $alpha$-RuCl3 and demonstrates a proof-of-principle method to detect fractional excitations in topological quantum materials.
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