In recent years, digital core technology as an emerging numerical simulation method has been widely used in various fields. This study investigates the unsaturated microscopic seepage of gas-water phases in the pore-throat structure of sandstone. First, the real three-dimensional pore-throat structure of sandstone is extracted by digital core CT scanning technique. Then, a 3D numerical model that used in the unsaturated microscopic seepage is established based on the visualization image processing technology. Next, the two-phase unsaturated seepage coupling equations are developed by using the two-phase volume-averaged momentum equation and the continuity equation. Finally, by combining the two-phase saturation relation, the van Genuchten model, and the Mualem model, we realize the simulation of the two-phase unsaturated seepage in a real pore-throat structure of sandstone. The results demonstrate that the effective porosity and permeability of the model are 14.97% and 21.5 mD, respectively. The variation of wetting phase saturation is not uniform due to the existence of dominant channels in the unsaturated seepage process. The streamlines at the large pore throat are denser than elsewhere, and the velocity of the fluid is faster. The relative permeabilities of the two phases at different positions in the model are similar. Moreover, the shape of the relative permeability curve is concave. The final relative permeability of the non-wetting phase is approximately equal to 1.