Graphitized carbon black 40b2 and acetylene black were filled separately in natural rubber matrix for preparing vulcanized rubber. The thermal conductivity of both kinds of composites was studied considering filler loading and temperature. SEM and TEM were applied to observe morphology of the filler and composites. The experimental results show that thermal conductivity of acetylene black/rubber composites is much better than that of graphitized carbon black 40b2/rubber composites, which is opposite to the electric conduction properties. As filler loading increased, the difference increased, and when the filler loading is up to 40phr, the thermal conductivity value of acetylene black/rubber composite is 53% larger than the other one. TEM shows that acetylene black has more botryoidal structure, larger carbon black aggregates in size, and much looser surface than 40b2.Moreover, for acetylene black, particles contact by surface mainly, and for 40b2, particles contact by point mainly. SEM shows that the distribution of carbon black 40b2 in rubber matrix is much better than acetylene black. The better thermal conductivity for acetylene black is attributed to the higher structure, nonuniform distribution in rubber matrix and surface contact between particles.