The surface morphology of GaN grown by MOCVD on GaN/Si template was studied. Rough morphology and deep pinhole defects on some surface areas of the samples were observed and studied. The formation of rough morphology is possibly related to Ga-Si alloy produced due to poor thermal stability of template at high temperature. The deep pinhole defects generated are deep down to the surface of MBE-grown GaN/Si template. The stress originated from the large thermal expansion coefficient difference between GaN and Si may be related to the formation of the pinhole defects. The surface morphology of the GaN can be improved by optimizing the GaN/Si template and decreasing the growth temperature.