Abstract The crystallization process had a great influence on the structure and catalytic performance of zeolites. In this paper, a series of Mordenite were synthesized and the variation of structure, morphology, skeletal atoms and acid sites distribution during the crystallization process were systematically studied. The characterization results indicated that the crystallization process of Mordenite could be separated into three parts: amorphous stage, rapid growth stage and slow growth stage. The Mordenite crystals experienced a reconstruction process when the relative crystallinity was already high in the slow growth stage. The skeletal atoms and acid sites distribution gradually changed although the relatively crystallization almost stayed the same in the reconstruction process. Besides, some small Mordenite crystals dissolved while some crystal planes continued to grow, forming larger Mordenite crystals and more mesopores through crystal stacking. Al atoms located in the strong acid sites or 8 member-ring channels were more preferentially dissolved out and re-entered the weak acid sites position or the 12 member-ring channels.