Monte Carlo (MC) simulations were performed to study the influence of framework protons on the adsorption sites of the benzene molecule in HY zeolite with different Si:Al ratios. Eleven types of adsorption sites were observed including five reported sites (H1, H2, U4, U4(H1), and W) and six newfound sites (W(2H1), U4(2H1), H1(H2), U4(H1,H1), H1(H2,H1), and U4(H1,H1,H1)), which were "supersites" with more than one proton. The stability order of the sites found in the 28Al model can be expressed as U4(H1,H1,H1) > U4(H1) > H1(H2,H1) > W(2H1) > U4(H1,H1) > H1(H2) > H1 > H2 > U4> U4(2H1) > W. Increasing number of zeolite protons resulted in an increasing proportion of supersites, which enhanced adsorption energies of sites. For FLY zeolite models containing different numbers of protons with the same ratio of H1:H2, the amount of the most stable adsorption sites containing HI proton increased, while the amount of the most stable adsorption sites containing H2 decreased, with increasing number of protons.