The ecological environment in southwestern China is fragile. Due to the significant preferential flow in vertical and horizontal directions and poor water conservation ability, vegetation degradation still exists under conditions of abundant rainfall. Therefore, the pore connectivity and infiltration characteristics in shallow soil under typical local vegetation need to be studied. A calculation model for the vertical connectivity of soil macropores was independently constructed, and differences in soil macropore structures and the degree of vertical connectivity in typical vegetation types (natural secondary forest, natural grassland, Yunnan pine plantation, eucalyptus plantation, cypress plantation, mulberry bushes) were investigated by CT scanning technology of undisturbed soil columns. The results showed that the vertical connectivity of large pores in the shallow soil of the region can be quantitatively described by X-ray tomography, and the total surface area and cumulative curvature of macropores in natural grassland soil were two or three times that in artificial vegetation. The concentration area of macropores in the soil of artificial forestland was closer to the surface, and the tendency of macropore preferred path decreased by 76.18% around 30 cm depth in the soil. The vertical connection of soil macropores in artificial forests was significantly lower than that of natural secondary forestlands (33.03%) and natural grasslands (36.75%). The restoration of the plantation improved surface soil pore structure, and the vertical connectivity of soil is nearly 20% less than that of natural vegetation types (natural secondary forestland, natural grassland), which reduced water outflow rate by nearly 44% and electrolyte content by nearly 14% at a depth of 30 cm. This study provided data and research directions for the study of hydrological processes in local forest vegetation and technical support for solving the problems of soil water loss and forestland water conservation in southwestern China.