Developing highly active hydrodesulfurization (HDS) catalysts is of great importance for producing ultraclean fuel. Herein we report on crystalline mordenite nanofibers (NB-MOR) with a bundle structure containing parallel mesopore channels. After the introduction of cobalt and molybdenum (CoMo) species into the mesopores and micropores of NB-MOR, the NB-MOR-supported CoMo catalyst (CoMo/NB-MOR) exhibited an unprecedented high activity (99.1%) as well as very good catalyst life in the HDS of 4,6-dimethyldibenzothiophene compared with a conventional γ-alumina-supported CoMo catalyst (61.5%). The spillover hydrogen formed in the micropores migrates onto nearby active CoMo sites in the mesopores, which could be responsible for the great enhancement of the HDS activity.