The NH4+/Na+ ions exchange process of analcime in (NH4)2CO3 solution using hydrothermal method and its kinetics were studied. X-ray diffraction (XRD), Fourier transformation infrared spectrometry (FTIR), and scanning electron microscopy (SEM) were applied to characterize the as-exchanged samples. Rietveld refinements were utilized to investigate crystallographic occupancy of NH4+ based on the XRD results and the crystal chemistry rules, showing that there exists isostructural crystal between analcime and ammonioleucite after ion-exchange although they belong to different crystal systems and nitrogen atoms surrounded by six oxygen atoms in ammonioleucite are located in the sites of water molecule in analcime. FTIR results indicated that disappearance of water molecule in the region of 3400–3500 cm−1 is caused by the escape of zeolite water from analcime (NaAlSi2O6·H2O) to ammonioleucite (NH4AlSi2O6) with the hydrothermal-treated temperature increased and time prolonged. The lower frequency of vibration at 3270 cm−1 as compared to buddingtonite indicates there exists relatively strong hydrogen bonding between ammonium ions and the framework environment. It turned out that the reaction rate was controlled by chemical reaction at lower temperatures (70 and 90 °C) and by product layer diffusion at higher temperatures (110 and 130 °C) from the experiments and analysis of kinetics according to shrinking core model.