The mechanisms of adsorption of methane (CH4) and carbon dioxide (CO2) are still a challenge in CO2 sequestration with enhanced gas recovery (CS-EGR) in shale gas reservoirs. In this study, we focus on the adsorption behaviors of CO2 and CH4 on kerogen type IIIA using molecular dynamics (MD) and Grand Canonical Monte Carlo (GCMC) simulations. Simulation results indicated that the difference between the adsorption capacity of CO2 and CH4 increased with increase of mole fraction of CO2. The adsorption capacity of CO2/CH4 decreased with increase of the water content. Water showed a greater effect on the adsorption of CO2 than on that of CH4. The isosteric heat and adsorption selectivity of CO2/CH4 decreased at low water content and increased with increasing water content. This study provides certain theoretical guiding significance for the application of CS-EGR projects from a microscopic perspective.