We report on a comprehensive theoretical and experimental investigation of thermal conductivity in indium-tin-oxide (ITO) thin films with various Ga concentrations (0–30 at. %) deposited by spray pyrolysis technique. X-ray diffraction (XRD) and scanning electron microscopy have shown a structural transformation in the range 15–20 at. % Ga from the nanocrystalline to the amorphous phase. Room temperature femtosecond time domain thermoreflectance measurements showed nonlinear decrease of thermal conductivity in the range 2.0–0.5 Wm⁻¹ K⁻¹ depending on Ga doping level. It was found from a comparison between density functional theory calculations and XRD data that Ga atoms substitute In atoms in the ITO nanocrystals retaining Ia-3 space group symmetry. The calculated phonon dispersion relations revealed that Ga doping leads to the appearance of hybridized metal atom vibrations with avoided-crossing behavior. These hybridized vibrations possess shortened mean free paths and are the main reason behind the thermal conductivity drop in nanocrystalline phase. An evolution from propagative to diffusive phonon thermal transport in ITO:Ga with 15–20 at. % of Ga was established. The suppressed thermal conductivity of ITO:Ga thin films deposited by spray pyrolysis may be crucial for their thermoelectric applications.