Flue gas flooding is one of the important technologies to improve oil recovery and achieve greenhouse gas storage. In order to study multicomponent flue gas storage capacity and enhanced oil recovery (EOR) performance of flue gas water-alternating gas (flue gas–WAG) injection after continuous waterflooding in an oil reservoir, a long core flooding system was built. The experimental results showed that the oil recovery factor of flue gas–WAG flooding was increased by 21.25% after continuous waterflooding and flue gas–WAG flooding could further enhance oil recovery and reduce water cut significantly. A novel material balance model based on storage mechanism was developed to estimate the multicomponent flue gas storage capacity and storage capacity of each component of flue gas in reservoir oil, water and as free gas in the post-waterflooding reservoir. The ultimate storage ratio of flue gas is 16% in the flue gas–WAG flooding process. The calculation results of flue gas storage capacity showed that the injection gas storage capacity mainly consists of N2 and CO2, only N2 exists as free gas phase in cores, and other components of injection gas are dissolved in oil and water. Finally, injection strategies from three perspectives for flue gas storage, EOR, and combination of flue gas storage and EOR were proposed, respectively.