The control over the configuration, size, and density of Au nanoparticles (NPs) has offered a promising route to control the spatial confinement of electrons and photons, as a result, Au NPs with a various configuration, size and density are witnessed in numerous applications. In this work, we investigate the evolution of self-assembled Au nanostructures on 4H-SiC (0001) by the systematic variation of annealing temperature (AT) with several deposition amount (DA). With the relatively high DAs (8 and 15 nm), depending on the AT variation, the surface morphology drastically evolve in two distinctive phases, i.e. (I) irregular nano-mounds and (II) hexagonal nano-crystals. The thermal energy activates adatoms to aggregate resulting in the formation of self-assembled irregular Au nano-mounds based on diffusion limited agglomeration at comparatively low annealing temperature, which is also accompanied with the formations of hillocks and granules due to the dewetting of Au films and surface reordering. At high temperature, hexagonal Au nano-crystals form with facets along {111} and {100} likely due to anisotropic distribution of surface energy induced by the increased volume of NPs. With the small DA (3 nm), only dome shaped Au NPs are fabricated along with the variation of AT from low to elevated temperature.