To reveal the influence of soil pore structure on meso-seepage mechanism, and find a simple and efficient research method, we selected the undisturbed granite residual soil in Fuzhou, Fujian as the research object to study the water-air two-phase coupling of meso-seepage in soil pores, based on computed tomography (CT) and virtual simulation APP development technology. The results showed that large pore preferential flow existed in the water-air two-phase seepage process, and the phenomenon of “detouring” tended to occur at the positions of high pore roundness. Affected by the parameters of water and air phases, some pores at the dead angles formed some closed space containing only air phase. The two-phase seepage velocity was mainly controlled by the curves of the pore channel, when the pore was straight and wide, the seepage velocity was relatively high, which eventually formed a “preferential channel”. The seepage velocity at the “detouring” part of the pore was far slower than that at the surrounding parts. Furthermore, the distribution of the two-phase seepage pressure fields in the soil mass were inhomogeneous. With the help of virtual simulation APP, the complex theoretical and physical fields can be easily encapsulated to present a user-friendly self-defined interface for the researchers to work with, which can greatly improve the efficiency of scientific research.