The thermal conductivity, thermal expansion coefficient and thermal diffusivity of PTFE composites filled with different contents of MWCNTs treated by different methods on surface were measured and analyzed. The thermal properties of PTFE composites filled with MWCNTs treated with different methods on surface were improved upon addition of MWCNTs. At higher temperature, the thermal conductivity and thermal diffusivity increased significantly. Microstructure of MWCNTs treated by different method on surface in PTFE was analyzed by transmission electron microscopy (TEM). The influences of each component in the composites and the inner structure on the change of overall thermal properties at different temperature fields were predicted.