Concerning the environmental and health problems related to SOx emission, the environmental protection agencies are incessantly tightening the permissible sulfur level in fuels such as gasoline and diesel. This gives a greater challenge for the traditional hydrodesulfurization (HDS), which is quite inefficient for removing refractory sulfur (RS) compounds (e.g., 4,6-dimethyldibenzothiophene). Consequently, the new efficient HDS catalysts for substituting the industrial HDS catalysts (Ni(Co)Mo/Al2O3) have received much attention. Zeolite-containing HDS catalysts are of particular importance because zeolites could alleviate the HDS of RS compounds via isomerization and cracking abilities of their Bronsted acid sites. The microporous zeolites slow down the diffusion of reactants and products, leading to uncontrolled cracking reactions that promote the coke formation and thus deactivate the HDS catalysts. Therefore, the application of zeolite-based catalysts was limited for HDS reactions in the early years. But, due to the introduction of hierarchical porous structure in zeolites, the cracking reactions catalyzed by strong Bronsted acid sites are controlled and uninterrupted molecular diffusion becomes highly possible. As a sequel, a better selectivity and improved HDS efficiency are attainable without any coke formation or with a reduced coke formation. Besides the porosity and acidity of zeolites, the synthetic methods and precursors of zeolite-based HDS catalysts and the mixing of zeolites with other supports like Al2O3 have impacts on the efficiency of zeolite-based HDS catalysts. In this review, all these factors are discussed along with the preparation methods of hierarchical zeolites and tuning methods of zeolite acidity. The process and catalyst details of traditional HDS are briefly explained at the outset. The types of metal active component present in various zeolite-based HDS catalysts and how their properties are influenced by zeolites are also summarized.