Over the past few decades, significant progress has been made to manipulate thermal transport in solids. Most of the effort has focused on reducing the phonon mean free path through boundary scattering. Herein, we demonstrate that the phonon confinement effect can also be used as a tool for managing thermal transport in solids. We measured the thermal conductivities of 10–70-nm-thick In0.53Ga0.47As nanofilms and found that the thermal conductivities decrease as the film thickness decreases. However, the reasons for this reduction differ for films with different thicknesses. The thermal conductivity of the 30- and 70-nm-thick In0.53Ga0.47As nanofilms decreases because of severe phonon boundary scattering. Our analysis indicates that phonon confinement occurs in the 10- and 20-nm-thick In0.53Ga0.47As nanofilms, which modifies phonon dispersion leading to changes in the phonon group velocity and the Debye temperature. These experimental and theoretical results could help to elucidate the phonon confinement effect in nanomaterials as well as establish a platform for understanding nanoscale thermal physics.