Conventional approaches are unable to describe phonon time-reversal symmetry () breaking. Here, we develop an framework, grounded in molecular Berry curvature (MBC) theory, that captures electronic-order-driven symmetry breaking in lattice dynamics. Using CoSnS as a model system, our framework yields phonon spectra that break both and mirror symmetries, quantitatively reproduce the observed phonon splittings observed in experiments, and reveal distinct microscopic origins for the and modes: splitting is governed by MBC and is accurately captured by our algorithm, whereas splitting is enhanced by the Fano resonance and matches the experimental data once the Fano-factor correction is included. Leveraging this algorithm, we predict several candidate materials with nonzero electronic-order-driven symmetry breaking in lattice dynamics, establishing a first-principles route to understand electron-phonon coupling, phonon magnetism, and related Hall-type lattice responses.

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