Sierpinski carpet fractal structure is introduced into the construction of Si/Ge nanocomposites in this paper so as to regulate and control the thermal conductivity of the nanocomposites. Non-equilibrium molecular dynamics simulation is applied to investigate the thermal conduction performance of nanocomposites embedded with fractal structure. Effects of the silicon atom percent, axial length and cross-sectional dimensions on the thermal conductivity of nanocomposites embedded with fractal structure are analyzed and compared with the corresponding nanocomposites embedded with traditional rectangular structure. It is indicated that, owing to the enhanced scattering at the Si/Ge interfaces of nanocomposites embedded with fractal structure, their thermal conductivity are lower than that embedded with rectangular structure, thus providing an effective way to improve the thermoelectric efficiency. And it is also demonstrated that the thermal conductivity of nanocomposites embedded with fractal structure are affected by the silicon atoms percent, axial length and cross-sectional size. The thermal conductivity is first decreased and then increased with the increase of Si atom percent. In addition, the increase in axial length of nanocomposites may lead to the enhancement of thermal conduction.