This paper deals with the Monte Carlo Simulation of the transport of high energy ions in materials, The incident high energy ions interact with the target material in a way is approximate to the two unrelated mechanisms, nuclear scattering and electronic process. The energy loss of incident ions due to nuclear scattering is calculated using binary collision approximation.The impact parameter is sampled and scattering angle can be derived. The electronic energy loss of incident ions for the high energy is calculated by Bethe-Bloch formulation. Lindhard-Scharff formulation is used for low energy and the interpolation formulation is used for the medium energy region. Finally, the computer simulation of high energy irons transport in aluminum and silicon is made, and the results are presented and analyzed.