Biogas, as a clean renewable energy, has been paid more and more attention. In this work, the simultaneous decarburization, desulfurization and dehydration of biogas with quaternary ammonium salt-based deep eutectic solvent (DES) was proposed for the first time. Based on COSMO-RS model, the separation performance of 100 DESs composed of 10 hydrogen bond acceptors and 10 hydrogen bond donors was screened by using Henry's law constant and selectivity coefficient as separation performance indexes. DESs composed of TEAC, TEAB, TEG and BDO were considered as the most promising candidate absorbents. Furthermore, the solubility of CH4 and CO2 in four DESs was measured at different temperatures and pressures. The results show that the selected DESs have excellent selective absorption performance for CO2. The regeneration experiment of the DESs showed that its CO2 absorption effect was almost unchanged after 5 absorption–desorption cycles. Molecular surface electrostatic potential (ESP) analysis was performed to obtain the binding sites of intermolecular interactions to reveal the separation mechanism of simultaneous decarbonization, desulfurization and dehydration of DESs. The interaction energy analyzed the hydrogen bond formation potential between different molecules. Independent gradient model based on Hirshfeld partition (IGMH) analysis showed that DESs mainly interacted with the components to be separated in the form of hydrogen bonds. The spatial distribution function (SDF) reveals the spatial distribution of different gases around DES from the perspective of cluster macromolecules. This provides theoretical insights of molecular thermodynamics and dynamics for the development of new DES for biomethane purification process.