In this work, ionic liquid (IL) as green solvent was first proposed for capturing methanol and dimethoxymethane (DMM) gases released in the fuel synthesis process. The hydrophilic IL [EMIM][BF4] was selected from 192 kinds of ILs by the COSMO-RS model. The separation mechanism was revealed at the molecule level in combination with the quantum chemistry calculation. The vapor-liquid equilibrium (VLE) data for the binary mixture of methanol (or DMM) and [EMIM][BF4] were experimentally obtained and compared with the prediction of UNIFAC-Lei model. It was found that the popular UNIFAC-Lei model can predict the VLE of the methanol + [EMIM][BF4] and DMM + [EMIM][BF4] mixtures well. Moreover, the methanol and DMM capture experiments using [EMIM][BF4] as absorbent were carried out, demonstrating the good separation performance. Furthermore, a rigorous equilibrium EQ stage model including the UNIFAC-Lei model parameters was built for simulating and optimizing the methanol and DMM capture processes using [EMIM][BF4] and the conventional benchmark solvent triethylene glycol (TEG) as absorbents at industry level. This work confirmed that capturing methanol and DMM gases with ILs is a typical process intensification method.