In this study, three micro/mesoporous composites with MCM-41 materials overgrowing on external surfaces of Y zeolite crystals were prepared. For the three composites, average crystal particle sizes of their zeolite components differed from each other, resulting from the different levels of alkali-treatments to the original Y zeolite before the composite synthesis. Hydroisomerization of n-dodecane (n-C12) was used to evaluate the catalytic performances of bi-porous Pt-loaded composite catalysts with similar metal-acid balances but different average zeolite crystal particle sizes, which leaded to the distinction of alkene intermediates' journey distances inside the acid-rich micropores between two accessible Pt metal sites on three catalysts. The number of protonic sites encountered by alkene intermediates along their diffusion paths, determining the skeletal transformation frequencies, was considered to be proportional to the above-mentioned intermediates' journey distances. Results showed that bifunctional catalysts with smaller average zeolite crystal particle sizes outperformed the catalyst containing the original Y zeolite in the regard of isomerization selectivity. This implied the significant effect of intermediates' journey distances within the microporous arrays between two Pt sites on bifunctional behaviors of catalysts. It can be confirmed that shortening this distance within certain limits indeed contributed to inhibiting secondary reactions, including the skeletal multiple branching and cracking.