Although the focus of shale gas recovery has shifted to CO2 sequestration with enhanced gas recovery (CS-EGR) for overcoming the low recovery efficiency, the adsorption and recovery mechanism of methane (CH4) and carbon dioxide (CO2 ) considering the effect of pore structures remains to be revealed. In this work, we focus on the influence of pore structures on adsorption behaviors of CH4 and CO2 at different geological depths and recovery process in different pore structures with various injection gas pressures. The results demonstrate that the excess adsorption capacity of CH(4 )and CO2 is in the order of cylinder-shaped > bottleneck > wedge-shaped > slit-shaped. The adsorption capacities of both CH4 and CO2 increase initially with geological depth until reaching maximum and then decrease with the depth going deeper. As for competitive adsorption of CH4 and CO2, the pore structures do not have much influence on the selectivity. However, the pore structures have significant impact on shale gas recovery, and the difficulty of CH4 molecules being displaced in various pore structures is ordered as cylinder-shaped > bottleneck > slit-shaped > wedge-shaped pores, which is consistent with the system resistance. The displacement efficiency of CH4 in cylinder-shaped pores is about 59%, much less than in other pore structures. The injection pressure has a negative effect on the speed of shale gas recovery and displacement efficiency of CH4 for the reason that more molecules aggregate into clusters near the pore throat and the flow blocking effect become more obvious when the injection pressure increases. Based on this actuality, we proposed a probable reliable method for CS-EGR: lower injection pressure is initially set to improve recovery efficiency, and higher pressure is finally used to increase CO2 sequestration amount.