High thermal conductive composite materials are widely used in to enhance heat dissipation. For the composite filled with non-spherical high thermal conductivity particles, the effective thermal property is not only dependent on components properties and particles volume fraction, but also on the particles orientation. In this paper, microstructure design of anisotropic material is focused on to make the effective thermal property as good as possible. Based on simulated annealing algorithm, we conduct a heat conduction optimization for a twodimensional composite material filled with short fibers. The optimization result is illustrated by the color contours corresponding to the optimized material fibers angles, and synthesized into representative anisotropic material microstructure. In addition, numerical calculations are conducted both on designed anisotropic material and homogeneous material with the same conditions. The result shows that compared with the homogeneous material case, a substantial reduction of the maximum temperature is found in the designed anisotropic material. When the input heat is 840 W/m2, the maximum temperature in the homogeneous material is 62.0 ºC, while in the anisotropic material the maximum temperature is 55.4 ºC.