Zr films (130 nm) were deposited on a 6H-SiC substrate at room temperature by sputter deposition. The interface solid-state reactions due to high vacuum thermal annealing between 600 °C and 850 °C for 30 min were investigated by Rutherford backscattering spectrometry (RBS) and X-ray diffraction (XRD). The surface morphology evolution due to thermal annealing was investigated and quantified using atomic force microscopy (AFM) and secondary electron microscopy (SEM). RBS analysis indicated that the as-deposited sample had a thin intermixed region consisting of ZrC and Zr2Si. The phases formed at each temperature were identified by XRD analysis. At temperatures of 700 °C and above, Zr reacted with the SiC substrate and formed a mixed layer of Zr carbide (ZrC) and Zr silicides (Zr2Si, ZrSi2 and Zr5Si3). The surface morphology from SEM analysis revealed a homogeneous Zr surface which varied with annealing temperature with the appearance of clusters on the Zr surface. AFM analysis revealed that the RRMS surface roughness decreased from the as-deposited value of 1.65 nm after annealing at 700 °C and then increased at higher temperatures due to coalescing of the surface granules in the Zr layer. It has also been demonstrated that the obtained experimental results between Zr and SiC have a good correlation with the ternary EHF model with regards to initial phases formed in the interface.