In this work, the mesoporous zeolite molecular sieve (ZMS, SBA-15) was modified by polyhedral ologomeric silsesquioxane (POSS) with sodium carboxylates(-COONa) and sodium sulphonate (-SO3Na) as ion-exchanging active group. With this approach, the capacity of removing ammonia-nitrogen (NH3-N) in water will be greatly increased because of changing and increasing of active groups. The exchangeing process between NH3-N and the active group in the pore of POSS modified SBA-15 including sodium silanolate (-SiONa), -COONa and -SO3Na was simulated by using Dmol3 program of the Materials Stutio (MS)software which is the quantum chemistry program based on density functional theory (DFT). In the simulation process the transition state of the exchanging reaction was searched with LST/QST algorithm and the activation energy of reaction was calculated. As the results of simulation and calculation, the activation energy of exchanging reaction between NH3-N and sodium sulphonate (-SO3Na) is smallest and the thermal effect of exchanging reaction between NH3-N and -SO3Na is lowest in all exchanging reactions, which means the exchanging reaction between NH3-N and -SO3Na proceeds more easily than others two exchanging reactions. The POSS-SO3Na is a better modifier for SBA-15 to remove NH3-N in water.