The usage of porous materials to remove Nano Particles (Nanoparticles, NPs) is one of the critical ways to purify the air. The present study employed three typical mesoporous structures, CMK-3, SBA-15 and MCM-41 to conduct removal experiments, in which NPs were generated, ranging from 2 nm to 20 nm, aiming at exploring the practical feasibility and relative theory foundation about the filtration of mesoporous structures towards NPs. Based on the physical and chemical characterization of the three mesoporous structures above, coupled with the adsorption experiments, the results acquired indicated that the most probable pore size of mesoporous structures coupled with certain mesoporous capacity of a mesoporous structure are the key to remove NPs. However, the distribution of micropore contributed hardly to the removal of NPs. Based on this, exploration was made to observe the effect that different flow rates and thicknesses had on the efficiency of NPs removal. The consequences showed that most penetrating particle size (MPPS) of NPs decreased with the increase of flow rates. Meanwhile, the corresponding removal efficiency of MPPS decreased. Furthermore, MPPS did not change with the change of thicknesses. This study provided technical evidence for the removal of NPs on mesoporous structures.