Deep space exploration technology is an important development direction for scientific exploration. The penetrator method has been proposed as an inexpensive method of studying planetary bodies. The basic principle of this method is that the detection equipment carried by the high-speed penetrator hits a planetary body at a high speed and is buried up to several meters below the surface to carry out detection work. During the frictional collision process with the planets crust, the instantaneous acceleration peaks of the scientific payload (electronic instrumentation) are large. Shock protection of these payloads is necessary to improve their survival and mission success. In this paper, with the goal of improving the survival rate of scientific loads inside a penetrator, a penetrator with a multilayer energy-absorbing structure is developed, in which cushioning protection measures, such as an aluminum foam-filled corrugated tube(AFFT) structure, polyurethane rubber, and epoxy resin potting, are applied to the penetrator. Since the analysis of this process is a highly nonlinear problem, a numerical modeling method is the main approach in this paper. The LS-DYNA software platform was used to simulate the penetrators penetration process on a moon soil medium. The results obtained using empirical formulas and theoretical derivations were compared with the results of numerical analysis to ensure the accuracy of the penetration simulation model. The finite element model of the penetrator was then verified and modified by conducting shock response spectral experiments and shock simulations. The results showed that the spacer scheme had a positive effect on the impact isolation and energy absorption. In addition, this scheme provides an important reference for the design of the penetrator prototype to guarantee the success of subsequent ground rocket sled experiments.