The surface morphology evolution of N-polar GaN with growth time was investigated and compared with Ga-polar GaN. N-polar GaN directly grown on SiC substrates was found to have slower 3D-to-2D growth transformation and less coalescence than the Ga-polar counterpart, resulting in rougher surface morphology, whereas the AlN nucleation layer accelerated 3D-to-2D transformation, resulting in smoother surface morphology. N-polar GaN was found to have mound-type surface morphology with clustered atomic steps, unlike the regular screw-type dislocation-mediated step-flow growth observed for Ga-polar GaN. This was explained by the lower diffusion of adatoms on the N-polar surface due to its higher surface energy and higher Ehrlich–Schwoebel barrier. In addition, the increased III/V ratio in N-polar GaN growth was found to reduce the surface roughness from 2.4 nm to 1 nm. Without Si doping, the N-polar GaN high electron mobility transistor (HEMT) heterostructures grown under optimized conditions with smoother surface morphologies exhibited a sheet carrier density of 0.91 × 1013 cm−2 and a mobility of 1220 cm2 (V s)−1. With Si δ-doping, the sheet carrier density was increased to 1.28 × 1013 cm−2 while the mobility was reduced to 1030 cm2 (V s)−1. These results are comparable to the state-of-the-art data of plasma-assisted molecular beam epitaxy-grown N-polar GaN HEMT heterostructures on SiC substrates.