In this work, a simple and efficient process for capturing methyl ethyl ketone (MEK) and sec-butanol (SBA) simultaneously in hydrogen (H-2) gas with ionic liquids (ILs) as absorbents is proposed. Based on a screening of ILs using the COSMO-RS model, the IL [EMIM][Tf2N] was chosen as a suitable candidate. The vapor-liquid equilibrium (VLE) for the MEK/SBA + IL system was measured and predicted by the UNIFAC model. Absorption experiments for MEK and SBA with IL were carried out at room temperature and atmospheric pressure. It was found that the IL ([EMIM][Tf2N]) exhibits a high absorption capacity for MEK and SBA. Moreover, the highly efficient separation performance is attributed to the formation of hydrogen bonds in the complexes, as explained by excess enthalpy analysis, interaction energy analysis, atoms in molecules topology analysis, electrostatic potential analysis, and independent gradient model analysis.