In desulfurization-related researchers, thiophene is widely studied in adsorption, separation, and catalysis processes as a typical sulfur-containing compound. However, the adsorption behavior of thiophene for the very first step of all processes still remains ambiguous. In this study, we proposed the loading dependence of the adsorption mechanism of thiophene in siliceous faujasite (FAU) zeolite using Monte Carlo simulations combined with the research of adsorption isotherms, density distributions, concentration profiles, radial distribution functions, and interaction energies. The results revealed that the thiophene adsorption mechanism in the whole loading range could be divided into two parts: "ideal adsorption" and "insertion adsorption", with the inflection point of the loading at 40 molecules/UC, which was similar to the adsorption of monoaromatics in zeolite. Below the inflection point, adsorbed thiophene distributed broadly and mainly occupied S and W adsorption sites ideally; after the inflection point, newly adsorbed thiophene molecules entered into the space near the center of the supercage with no influence on previously adsorbed ones. As the loading of thiophene increased, the adsorption amount on the S sites went up consistently over the entire loading range. By contrast, the adsorption amount on the W sites grew first and then dropped gradually for loadings below the inflection point. Finally, it decreased noticeably with loading close to saturated adsorption. In addition, the occurrence of the inflection point was due to the change of the dominated interaction energy.