A series of model probes with different sizes and polarity, such as ammonia, pyridine, and thiophene, have been used to gain insight into the influence mechanisms of extraframework aluminum (EFAl) species on the properties of Bronsted acid sites (BASs) in HY zeolites by periodic DFT calculation. EFAl species enhance the intrinsic strength of BAS in HY zeolites similar to the generally accepted results. However, the presence of EFAl species induces a significant deviation of a correlation between the adsorption energies of the probe molecules and the changes in intrinsic acidity characterized by DPE. These results demonstrate that EFAl species exert the additional forces (dispersion forces) on the probe molecules adsorbed on the BAS. In this work, a principal finding is by using a weaker polarity and right fit size molecule (that of thiophene in this work) as a probe can reveal the synergistic mechanisms between the EFAl species and the BAS.