The diffusion trajectory of NH4+, the configuration of NH4+ and water molecular in hydrated clinoptilolite and K+-NH4+ ion exchange process in the channel of clinoptilolite were simulated using the Materials Studio 4.3 software package’s CASTEP module. The results show that among these four hydrogen atoms in NH4+, only one is involved in the effective hydrogen bond with the oxygen atom in the framework. It was also proved that changing the distribution of the Al-site has no influence on the distribution of the extra-framework of NH4+. The interaction between particles in the channel and the zeolite framework causes the K+-NH4+ ion-exchange process to take place, which means that clinoptilolite possesses better selectivity to K+ than to NH4+. The structure parameters of the final product agree well with the reference, which indicate the formation of K-clinoptilolite.