The soil hydrological process plays an important role in transporting and distributing water in soils. However, the correlation between water flow behaviors, soil physical properties, infiltration patterns of soil exhibiting different soil layers, and the variation patterns in water flow behavior in rubber-based agroforestry systems remain poorly understood. Here, we mainly used dye-tracer infiltration to classify water flow behavior and HYDRUS-3D to interpret variation patterns of water flow behaviors in a rubber-based agroforestry system in southwest China. The results showed that (1) the soil of forestry patches under Hevea brasiliensis (HB) and Citrus reticulata (CR) exhibited better soil physical properties than those with no vegetation (NV). Compared with these in the NV, the saturated soil water content and field capacity increased by 15% and 21% in CR, and by 2% and 12% in HB, respectively; while the saturated hydraulic conductivity enhanced by 584% (p < 0.001) in the CR plot and by 226% (p < 0.001) in the HB plot. Correlation analysis shows that the soil bulk density, noncapillary porosity and capillary porosity significantly affected the field capacity, saturated water-holding capacity, and saturated hydraulic conductivity. (2) the general infiltration capacity of the whole soil profile, its order of continuity and the degree of connectivity of preferential flow path networks followed the order of CR > HB > NV. Finally, (3) the infiltration flow in soil under HB and CR exhibited a faster downward wetting front and an obvious lateral flow. These infiltration patterns compensated for the insufficiency of soil water in NV and finally caused water redistribution to be more homogenized across the whole soil profile. Therefore, our findings indicated that the rubber-based agroforestry system is a successful approach for conserving water and reducing runoff in tropical regions.