The relations between the buffer leakage current and the characteristics of nucleation layer of AlGaN/GaN heterostructure have been obtained by comparative study of depletion capacitance of C-V characteristics in GaN-based heterostructure. The results showed that, the heterostructure material based on a sapphire substrate with a low-temperature GaN nucleation layer and SiC substrate with a high-temperature AlN nucleation layer have smaller buffer leakage current and lower carrier concentration of the background GaN buffer layer than that based on a sapphire substrate with a low-temperature AlN nucleation layer. A thorough analysis shows that, there is an n-type GaN conductive layer near the GaN/substrate interface in buffer layer based on the thinner nucleation layers. Contrarily, high resistivity GaN buffer layers appear in heterostructure materials based on thicker nucleation layer. One of the main causes of device leakage is the n-type GaN conductive layer. Appropriately improving the quality and thickness of nucleation layer can effectively reduce the carrier concentration, raise the resistivity and suppress the leakage current of the GaN buffer layer.