The knowledge of adsorption behaviors and mechanism of CO2/CH4 in organic matter is of great importance for CO2 geological sequestration with enhanced gas recovery in shale reservoirs. In this study, the adsorption behaviors and confinement effects of CO2/CH4 in realistic kerogen nanopores have been investigated by using the grand canonical Monte Carlo method. To represent realistic nanopores in the kerogen matrix, the inkbottle-shaped and slit-like nanopores were developed. The effects of temperature, pressure, and pore size on competitive adsorption behaviors and adsorption mechanism of CO2/CH4 were explored. Simulation results indicate that the adsorption capacity of CH4 is lower than that of CO2 in the kerogen matrix with/without kerogen nanopores. A higher pressure and lower temperature are favorable for the adsorption capacities of CO2 and CH4. The gas adsorption capacities have been enhanced in both the inkbottle-shaped and slit-like nanopores. Meanwhile, the existence of inkbottle-shaped micropores is favorable for improving the selectivity of CO2/CH4 in shale organic matter. A higher CO2 injection pressure could improve its adsorption capacity but lower the adsorption selectivity of CO2 over CH4. Furthermore, confinement effects were observed in inkbottle-shaped and slit-like kerogen micropores and small mesopores. Two major factors, including the supercritical state of gas and microscale pores, could enhance the confinement effects. In addition to monolayer adsorption, micropore filling was observed in inkbottle-shaped and slit-like kerogen nanopores because of the confinement effects. It is expected that these results could help in understanding the microscopic adsorption mechanism and provide fundamental information for shale gas exploitation and CO2 sequestration.