The adsorption behavior and the mechanism of a CO2/CH4 mixture in shale organic matter play significant roles to predict the carbon dioxide sequestration with enhanced gas recovery (CS-EGR) in shale reservoirs. In the present work, the adsorption performance and the mechanism of a CO2/CH4 binary mixture in realistic shale kerogen were explored by employing grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations. Specifically, the effects of shale organic type and maturity, temperature, pressure, and moisture content on pure CH4 and the competitive adsorption performance of a CO2/CH4 mixture were investigated. It was found that pressure and temperature have a significant influence on both the adsorption capacity and the selectivity of CO2/CH4. The simulated results also show that the adsorption capacities of CO2/CH4 increase with the maturity level of kerogen. Type II-D kerogen exhibits an obvious superiority in the adsorption capacity of CH4 and CO2 compared with other type II kerogen. In addition, the adsorption capacities of CO2 and CH4 are significantly suppressed in moist kerogen due to the strong adsorption strength of H2O molecules on the kerogen surface. Furthermore, to characterize realistic kerogen pore structure, a slit-like kerogen nanopore was constructed. It was observed that the kerogen nanopore plays an important role in determining the potential of CO2 subsurface sequestration in shale reservoirs. With the increase in nanopore size, a transition of the dominated gas adsorption mechanism from micropore filling to monolayer adsorption on the surface due to confinement effects was found. The results obtained in this study could be helpful to estimate original gas-in-place and evaluate carbon dioxide sequestration capacity in a shale matrix.