β-(AlxGa1-x)2O3 (AGO) alloys offer transformative potential for high-power electronics, yet their thermal properties necessitate further research to enable electro-thermal co-design. Persistent challenges in accurately modeling atomic-scale disorder and in synthesizing compositionally graded AGO ternary alloy thin films fundamentally limit the mechanistic elucidation of alloy phonon transport through synergistic theory-experiment frameworks. By integrating neural evolution potential molecular dynamics with transient thermoreflectance experiments, we resolve the spectral phonon behaviors across million-atom disordered systems. Results reveal a two-regime thermal conductivity (TC) reduction: a sharp 43 % drop at x = 0–0.1 (7–4 W m−1 K−1) driven by suppressed low-frequency phonons (0–10 THz, 76 % loss), followed by a gradual 18 % decline at x = 0.1–0.5 (4–3.3 W m−1 K−1) via mid-frequency (10–15 THz) spectral compensation. Crystal orbital Hamilton population analysis reveals that the Al-O bond is strengthened and a reduction in atomic mass elevates the mid/high-frequency phonon density of states (PDOS), slowing TC degradation. The Virtual Crystal Approximation (VCA) simulation-based fitting to molecular dynamics results quantitatively resolves the dominance of strain-field scattering (>60 %) over mass-defect effects, a phenomenon driven by Al-induced bond-length mismatch and lattice symmetry breaking. This mechanism is experimentally corroborated by Raman spectral extinction of Ga2O3-characteristic phonon modes for x ≥ 0.1. Similarly, the thermal boundary conductance (TBC) of AGO/Al2O3 exhibits concentration-independent stability (<10 % variation for x > 0.1), resulting from PDOS redistribution-driven spectral coupling. This work provides atomic-scale insights into phonon engineering strategies for AGO-based power electronics, highlighting the critical role of frequency-resolved phonon manipulation in electro-thermal co-design.
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