Tribological mechanism of the diatom frustule with multi-layers of pores is studied with the liquid-solid interaction (FSI) method. Based on the reconstructed representative Coscinodiscus sp. frustule with two-layer porous structure, the tribological performances for the diatom frustule at its different pore diameter ratios, pore depth ratios, and velocities are solved through governing equations involved with FSI method. The numerical result shows that the existence of the two-layer porous structure of the diatom helps to reduce the friction between it and ambient water, and to increase its ability to resist the ambient water pressure. The two-layer porous structure effectively improve the tribological performances for the diatom frustule due to the change in the frustule velocity.