In this paper, Levenberg-Marquard algorithm was used to simulate thermal performance of aligned carbon nanotubes-filled rubber composite, and the effect of temperature, filling amount, MWNTs orientation and other factors on thermal performance were studied. The research results showed: MWNTs orientation can greatly improve the thermal conductivity of composite materials, the thermal performance improvement of overall orientation was higher than the local orientation. Volume fraction can affect thermal performance, thermal conductivity increased with the increase of volume fraction. Temperature had no significant effect on the thermal conductivity. The simulation results correlated well with experimental results, which showed that the simulation algorithm is effective and feasible.