Incorporation of heteroatoms into the framework of zeolites has become a significant strategy to improve their performance in catalysis and adsorption, because the obtained heteroatom zeolites exhibit quite different properties from the conventional aluminosilicate zeolites in aspects of surface acidity, pore structures, particle size and so on. In this review, the progress on the heteroatom zeolites including their synthesis and application is highlighted. First, the recent advance on the design and synthesis of different heteroatom zeolites is summarized. Special emphasis is placed on the introduction and comparison of three typical methods, including the direct synthesis, post synthesis and improved direct synthesis, for the traditional heteroatom zeolites (such as TS-1, Sn-MFI, Sn-β) and newly-reported heteroatom zeolites (such as W-MFI, Mo-MFI). According to their intrinsic characteristics, the application of heteroatom zeolites in diverse fields, such as production of fine chemicals, air pollution control and biomass conversion is then discussed. Finally, the challenges and perspective on the future development of heteroatom zeolites in low-cost preparation and practical application are proposed.