Design and preparation of highly active hydrodesulfurization (HDS) catalysts is very important for the removal of air pollution. Herein, we report an extraordinarily active HDS catalyst, which is synthesized by loading of Pd on mesoporous zeolite Y (Pd/HY-M). The mesoporous zeolite Y is successfully synthesized using a water glass containing N,N-dimethyl-N-octadecyl-N-(3-triethoxysilylpropyl) ammonium [(C(2)H(5)O)(3)SiC(3)H(6)N(CH(3))(2)C(18)H(37)](+) cation as a mesoscale template. Compared with mesoporous Beta and ZSM-5 supported Pd catalysts (80.0% and 73.4% for Pd/HBeta-M and Pd/HZSM-5-M, respectively) as well as commercial catalyst of γ-Al(2)O(3) supported Pd catalyst (31.4%), Pd/HY-M catalyst exhibited very high activity in HDS of 4,6-dimethyldibenzothiophene (4,6-DM-DBT, 97.3%). The higher activity of Pd/HY-M than that of Pd/HBeta-M and Pd/HZSM-5-M is assigned to the larger micropore size of zeolite Y compared to that of Beta and ZSM-5. Theoretical simulation and adsorption experimental data show that 4,6-DM-DBT has difficulty entering the micropores of ZSM-5 and Beta zeolites, but the micropores of Y zeolite are accessible.