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The initial stage of high intensity pulsed ion beam irradiated magnesium alloys was studied by MD simulation. Specimens containing Mg 17 Al 12 precipitation were modeled to investigate the evolution of magnesium alloys during several picoseconds after a high-energy ion impacting. It was found that the Mg 17 Al 12 precipitation has little effects on the kinetic energy evolution in the heat zone, but considerable effects on strength of kinetic energy peak moving to the deep matrix and on the surface morphology of the magnesium alloy at thermal equilibrium state. The thickness of the heat zone is independent on the temperature of surface region.