Zeolites Y were modified by ion-exchange method, and their structural properties were examined using N-2 adsorption, Fourier transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and chemical composition analysis. The dynamic adsorption of methyl mercaptan (CH3SH) on different ion-exchanged zeolites Y was conducted on a fixed-bed adsorption column. The effects of gas hourly space velocity, operation temperature, and composition of the feed gas on the performance of CH3SH adsorption on ion-exchanged zeolites Y were studied carefully. Furthermore, the adsorption mechanism for CH3SH and CO2 adsorption on ion-exchanged zeolites was revealed by using density functional theory (DFT) calculation methods. Among all the ion-exchanged samples, CuY holds the highest CH3SH breakthrough adsorption capacity, q, of up to 70 mg/g. When using natural gas containing 4% CO2 as the feed, q of CuY was slightly reduced to 64 mg/g. The DFT calculation results indicate that the SM bond is formed between CH3SH and Cu2+ during CH3SH adsorption, which benefits the adsorption of CH3SH on CuY zeolite. Moreover, the DFT calculation suggests the weak CuO bonding interaction formed in the adsorption of CO2 on CuY, the interaction of which releases much less energy compared with CH3SH adsorption. The CH3SH-saturated CuY sample can be regenerated by thermal treatment under air atmosphere at 350 degrees C. After six adsorptionregeneration cycles, the regenerated CuY shows q of 55 mg/g, which is 21.4% lower than that of the fresh sample.