To reveal the influence of acid sites with different spatial locations of USY zeolite with different micro-/mesoporous structures and Si/Al ratio, catalytic cracking of methylcyclohexane on the zeolites is employed to study the synergism effects of acid sites and porous structures (“active region”) in the hierarchical USY zeolites. The results showed that the hierarchical USY zeolites have increased numbers of accessibly strong Brønsted acid sites and greatly enhanced diffusion ability due to the hierarchical pore-structure, resulting in mainly monomolecular protolytic scission in cracking reactions and less bimolecular hydrogen transfer. The isomerization reaction is from intramolecular transalkylation and the isomerics are the intermediates of the cracking reaction. The protolytic cracking that occurs in hierarchical high-silica USY-zeolites follows the Haag-Dessau cracking.