Organic clathrates, particularly those formed by hydroquinone (HQ) and gas mixtures, have been far less studied than other inclusion compounds, such as gas hydrates. In this study, experiments and molecular dynamics simulations were performed on mixed (CO2 + CH4)–HQ clathrates. Single crystals were synthesized using gas mixtures with different compositions, ranging from pure CO2 to pure CH4. The crystal structure, the guest occupancy in the clathrates, and the variation of the crystal lattice parameters according to clathrate composition were obtained by X-ray diffraction measurements. In addition, molecular dynamics simulations were performed on the same systems, with state-of-the-art molecular models and force fields. The experimental results obtained and the molecular dynamics simulation estimations were in good agreement. The clathration selectivity was also calculated on the basis of experimental results, and the composition of the solid phase was correlated with the composition of the gas phase at equilibrium. These new insights into these structures will be useful from both a fundamental and a practical point of view, particularly for further developing innovative gas separation techniques using HQ clathrates.