Underground gas storage (UGS) is a beneficial economic method of compensating for the imbalance between natural gas supply and demand. This paper addresses the problem of a lack of research on the two-phase distribution pattern and seepage law during the water–gas alternated flooding in gas storage reservoirs. The study constructed a three-dimensional digital core of the aquifer reservoir based on Computed Tomography (CT) scanning technology, and extracted the connecting pore structure to establish the tetrahedral mesh model. A two-phase microscopic seepage model was established based on the Volume of Fluid (VOF)method, and microscopic gas and gas–liquid two-phase unsaturated microscopic seepage simulation was carried out. The results show that the effective reservoir capacity increases with the increase in the number of alternated flooding cycles. The irreducible water is mainly distributed in the dead-end of the pore space and small pore throats, and the residual gas is mainly distributed as a band in the gas–water interface and the dead-end of the pore space of the previous round. The reservoir capacity can be increased by appropriately increasing the intensity of injection and extracting and decreasing the pressure of the reservoir.