Thickness dependency and interfacial structure effects on thermal properties of AlN thin films were systematically investigated by characterizing cross-plane and in-plane thermal conductivities, crystal structures, chemical compositions, surface morphologies and interfacial structures using an extended differential 3ω method, X-ray diffraction (XRD) analysis, X-ray photoelectron spectroscopy, atomic force microscopy (AFM) and transmission electron microscopy. AlN thin films with various thicknesses from 100 to 1000 nm were deposited on p-type doped silicon substrates using a radio frequency reactive magnetron sputtering process. Results revealed that both the cross- and in-plane thermal conductivities of the AlN thin films were significantly smaller than those of the AlN in a bulk form. The thermal conductivities of the AlN thin films were strongly dependent on the film thickness, in both the cross- and in-plane directions. Both the XRD and AFM results indicated that the grain size significantly affected the thermal conductivity of the films due to the scattering effects from the grain boundary.