In this work, the mesoporous zeolite molecular sieve (ZMS) surface was modified using polyhedral ologomeric silsesquioxane (POSS) with carboxyl sodium terminal groups (POSS−COONa) as ion-exchange active groups. The characterization of the POSS−COONa structure by standard techniques (such as SEM, TEM, XRD, etc.) was investigated and discussed. With this approach, the exchange capacity of ammonia-nitrogen (NH3-N) in water would be greatly increased. The diffusion behavior of NH3-N in the pores of POSS-modified ZMS was calculated using a molecular dynamic simulation (MDS) program of the Materials Stutio (MS) software which facilitate to study the effect of POSS modification on pore structure and exchange capacity. The interface binding energy between POSS−COONa and ZMS was calculated using MDS, facilitating the study of a simple regeneration method for exchanged active groups. It was estimated that the weight of the POSS-modified ZMS could be reduced by 25% for the same 90% of NH3-N removal rate of the normal ZMS under the same conditions. If the removal rate of the normal ZMS for a higher concentration of NH3-N in water was 60%∼70%, the removal rate of the POSS-modified ZMS could be up to 80%∼90%.