The long-term cultivation of banana crops (Musa nana Lour.) has caused soil and water resources improper utilization. However, the effect of banana plantation regime on soil water flow pattern is still poorly understood. This study focused on the dominant pattern of soil water movement in the 1-year (B1) and 4-year (B2) banana plantations. The results showed that (1) the soil physical properties showed variability with soil depths, especially obvious changing from surface to 40 cm depth, which had restriction on soil infiltration in different depths. (2) The saturated hydraulic conductivity (Ks) decreased with the increasing distance from the banana trunk. Moreover, the Ks in the B2 plot increased by 65.5% compared to the B1 plot at the soil layer 0–20 cm. (3) Preferential flow was the main path of soil water transport and was significantly influenced by soil bulk density, porosity and root systems. Redundancy analysis (RDA) showed that banana root biomass was the most prominent factor influencing the dyeing area. (4) The soil infiltrability and the preferential flow degree of both B1 and B2 plots were stronger in the root zone than those in the non-root zone. Such results were attributed to the root systems around the banana trunk that were more developed than those far away from the trunk; a large number of pore channels formed around the root systems that promoted the preferential flow. Thereby, our results suggest that banana root was the important factor affecting soil water movement. The improvement in root network of banana plantation regime can result in better soil physical properties. This knowledge will be vital for the sustainable cultivation and irrigation of banana crops.