Surface morphological features and nanostructures generated during SiC graphitization process can significantly affect the fabrication of high-quality epitaxial graphene on semiconductor substrate. In this work, the surface morphologies and atomic structures during graphitization process of 4H-SiC (0001) have been studied by using scanning tunneling microscopy. Our high-magnified STM images exhibit the appearance and gradual developments of SiC (1×1) nanostructures after 1100 °C cleaning treatments, irregularly distributed among carbon nanocaps and (√3×√3) reconstruction domains. A model for the formation and growth progression of SiC (1×1) nanostructures has been proposed. When post-annealing temperature reaches 1300 °C, the nano-holes and nano-islands can be observed on the surface and multilayer graphene is often detected lying on the top surface of those nano-islands. These results provide profound insights into the complex evolution process of surface morphology during SiC thermal decomposition and will shed light on the fabrication of SiC nanostructures and graphene nanoflakes.