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 (CH 3 SH) 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 CH 3 SH adsorption on ion-exchanged zeolites Y were studied carefully. Furthermore, the adsorption mechanism for CH 3 SH and CO 2 adsorption on ion-exchanged zeolites was revealed by using density functional theory (DFT) calculation methods. Among all the ion-exchanged samples, Cu−Y holds the highest CH 3 SH breakthrough adsorption capacity, q, of up to 70 mg/g. When using natural gas containing 4% CO 2 as the feed, q of Cu−Y was slightly reduced to 64 mg/g. The DFT calculation results indicate that the S−M bond is formed between CH 3 SH and Cu 2+ during CH 3 SH adsorption, which benefits the adsorption of CH 3 SH on Cu−Y zeolite. Moreover, the DFT calculation suggests the weak Cu−O bonding interaction formed in the adsorption of CO 2 on Cu−Y, the interaction of which releases much less energy compared with CH 3 SH adsorption. The CH 3 SH-saturated Cu−Y sample can be regenerated by thermal treatment under air atmosphere at 350 °C. After six adsorption− regeneration cycles, the regenerated Cu−Y shows q of 55 mg/g, which is 21.4% lower than that of the fresh sample.