Currently the investigations on room-temperature thermal conductivity of single crystal SiC and the dependence of thermal conductivity on temperature show some differences. What’s more, most researches relating to the thermal conductivity of single crystal SiC concentrate on the crystalline orientation along c-axis <0001> or vertical to c-axis randomly, which can’t account for the anisotropy of thermal conductivity for SiC rigorously. In this paper, the effect of impurities and defects on thermal conductivity of single crystal 4H-SiC and 6H-SiC in three accurately different directions were studied. These samples (sized 12.7 mm×3 mm) along <1100>, <1120>, <0001>, respectively cut from a 4H-SiC and 6H-SiC single crystal were characterized by flash method in order to get their thermal diffusion. The thermal conductivity was derived from the product of thermal diffusion and specific heat. Impurities and defects of these samples were characterized by glow discharge mass spectroscope (GDMS) and scanning electron microscope (SEM), respectively. The experimental results indicate that the thermal conductivity of single crystal SiC along <1100>, <1120>, <0001> decreases with increasing the temperature, while the thermal conductivity along <0001> is the smallest among all samples. And the thermal conductivity of 6H-SiC is abnormally larger than that of 4H-SiC as a result of many of impurities within 6H-SiC. Therefore, defect has more obvious effect on the thermal conductivity of single crystal than impurity, which is the reason for the anisotropy of thermal conductivity.