In this work, the mesoporous zeolite molecular sieve (ZMS, SBA-15) was prepared by rice hull ash (RHA) and the surface of ZMS pore was modified by (3-mercaptopropyl) trimethoxysilane (MCPMS) with sulfhydryl (SH) as active group connecting to the SBA-15 pore surface. The capacity of removing ammonia-nitrogen (NH3-N) in water will be increased because of the increasing in adsorption active groups. The micro-structures of SBA-15-SH were characterized by FTIR, SEM, TEM, SAXRD. The diffusion and adsorbed behavior of NH3-N in pores of the modified ZMS was simulate by using a molecular dynamic simulation (MDS) program of the Materials Studio software (MSS) which facilitated study of the effect of this modification on pore structure and adsorption capacity. As results of the experiments, the MCPMS-modified ZMS showed more efficient in removing NH3-N in drinking water than before the modification under the same conditions.