Flue gas poses subsurface direct storage inefficiency due to its high non-CO2 2 content, while surface separation, desulfurization and denitrification processes require additional equipment and financial resources. To address these challenges, flue gas subsurface component separation and CO2 2 sequestration within aquifer were proposed in this paper. CO2 2 migrates notably slower than N2, 2 , leading to the gathering of N2 2 at gas flooding front and the occurrence of CO2 2 hysteresis during flue gas filtration within the aquifer. The phenomenon, characterized by gas composition deviations from the original injection mole fractions of N2 2 and CO2, 2 , is referred to as the flue gas component separation. Numerical simulation results indicate that the solubility difference between N2 2 and CO2 2 is the primary force driving the separation of components, and the asynchronous filtration velocities of the gas and aqueous phases further promote the separation. Thus, simultaneous N2 2 separation and CO2 2 storage can achieve by the optimized gas-water alternate injection, and the efficiencies of N2 2 separation and CO2 2 storage are inversely correlated. Increasing N2 2 mole fraction within the injected flue gas enhances the efficiency of N2 2 separation, while having a slight effect on CO2 2 storage. Water vapor in flue gas condenses and integrates into the liquid phase, while O2 component 2 component is produced slightly later than N2, 2, leading to a marginal reduction in N2 2 separation efficiency. The synergistic influences of aquifer temperature and pressure exhibit bidirectionality, stemming from the shift between the dominant factors between CO2 2 dissolution and gas sweep efficiency. Conditions of relatively lower aquifer temperatures and moderate pressures, particularly in medium permeability aquifers, are more favorable for enhancing N2 separation 2 separation and CO2 2 storage. This proposal method holds the potential for efficient subsurface separation of flue gas components and concurrent underground storage of CO2, 2 , thereby contributing to the reduction of greenhouse gas emissions and mitigation of climate change.