Controlling heat flow in β-Ga₂O₃ thin films requires understanding both phonon transport within the semiconductor and heat transfer across metal/semiconductor interfaces. Here, we investigate these pathways in high-temperature RF magnetron-sputtered β-Ga₂O₃ films grown on c-plane sapphire with thicknesses from 0.42 to 2.1 μm. The thermal conductivity increases from 5.4–6.9 W m⁻¹ K⁻¹ in the 420 nm film to approximately 10–12 W m⁻¹ K⁻¹ in the thicker films. Structural characterization reveals thickness-dependent microstructural evolution, including grain coarsening and intergranular void-like defects. A semi-analytical Debye–Klemens model incorporating phonon scattering from film boundary and defects reproduces the overall thickness dependence. We further demonstrate that Ar plasma treatment provides an effective means of modifying interfacial heat transfer: the Al/β-Ga₂O₃ thermal boundary conductance increases from approximately 60 to 100 MW m⁻² K⁻¹, or by about 70%, while the thermal conductivity of the underlying β-Ga₂O₃ remains comparatively unchanged. Picosecond laser ultrasonic measurements and cross-sectional TEM reveal a corresponding modification of the interfacial acoustic response and formation of an ultrathin amorphous/disordered near-surface region. These results demonstrate that thermal transport in sputtered β-Ga₂O₃ can be independently tuned through film-thickness-dependent microstructure and near-surface interface modification, providing practical routes for thermal management in β-Ga₂O₃-based devices.