Controlling the product selectivity of the hydrocracking process is of great significance in the petroleum refining process. In this study, in contrast to a commercial Y zeolite, an in situ crystallized Y zeolite on kaolin was prepared to investigate the effects of mass transfer performance of the cracking active component on the hydrocracking properties of vacuum gasoil (VGO). The texture properties and acid sites accessibility were analyzed and evaluated by using SEM, TEM, Ar adsorption isotherms, and in situ FT-IR spectra techniques. The frequency response (FR) method was used to investigate the mass transfer performance of the two Y zeolites by using benzene as probe molecule. The results reveal that the variations in crystal morphology and pore architecture led to marked differences in the mass transfer performance and acidity accessibility of Y zeolites. Notably, the aromatic contents in middle distillate are higher; however, the Bureau of Mines Correlation Index (BMCI) values of tail oil are lower for the hydrocracking products from the HY-kaolin zeolite-based catalyst than that from a comparative sample. So, it can be inferred that the product distribution is significantly affected by the structural characteristics of Y zeolite as the cracking active component. The improved accessibility of Bronsted-acid sites for the bulky molecules could promote the ring-opening reactions of bulky molecules, and the reduced diffusion path length in Y zeolites can suppress the excessive hydrogenation and secondary cracking of the primary products.