The influence of the surface morphology on the channel mobility of 4H-SiC metal-oxide-semiconductor field effect transistors annealed under two different conditions is discussed. The devices were fabricated using post-implantation annealing at 1650 °C. In particular, while the use of a protective capping layer during post-implantation annealing preserved a smooth 4H-SiC surface resulting in a channel mobility of 24 cm2 V−1 s−1, a rougher morphology of the channel region (with the presence of surface macrosteps) was observed in the devices annealed without protection, which in turn exhibited a higher mobility (40 cm2 V−1 s−1). An electrical analysis of SiO2/SiC capacitors demonstrated a reduction of the interface state density from 7.2 × 1011 to 3.6 × 1011 cm−2 eV−1, which is consistent with the observed increase of the mobility. However, high resolution transmission electron microscopy showed an almost atomically perfect SiO2/4H-SiC interface. The electrical results were discussed considering the peculiar surface morphology of the annealed 4H-SiC surfaces, i.e., attributing the overall reduction of the interface state density to the appearance of macrosteps exposing non-basal planes.