In order to investigate the effects of different water regulations on the root spatial distribution, water consumption, water use and other indexes in a typical alley cropping system comprising apple (Malus pumila)-soybean (Glycine max), an experiment of mulching and irrigation coupling was carried out in the Loess Plateau of Shanxi Province. Three levels of irrigation thresholds were set:55% (low, W1), 70% (medium, W2), and 85% (high, W3) of field capacity. Meanwhile, two mulching materials including straw (M1) and plastic film (M2) were also set. The results indicated that the water regulation increased the total root length density of apple and soybean, and also expanded the root length distribution of apple in horizontal and vertical directions. The apple root length density was negatively correlated with the distance from the tree row while the soybeans had positive correlation, and both the crops had negative correlations with the vertical depth. The distribution of soil moisture increased first with the distance from trees to the crops then decreased at grain filling stage, and the minimum values occurred in the distance of 1.5~2.0 m away from the tree line. Compared with clean tillage treatment (CK0) and single mulching treatment (CK1 and CK2), the water regulation treatments increased the soil moisture in 0-60 cm depth significantly. The cluster analysis showed that the main competition area in soil moisture for the two plants was in the distance 0.5~1.5 m away from the tree row with soil depth of 0-40 cm. The apple fine roots in the M2W2 treatment were concentrated in 20-40 cm soil layer while the soybeans' in 0-20 cm soil layer, which alleviated water competition between the two species. Additionally, the water consumption in M2W2 could be reduced by 40~50 mm compared with W3 and the yield and water use efficiency could be increased by 29.37%~41.92% and 12.29%~53.35%, respectively, compared to other water regulation treatments. The net income could be 2 976.5 yuan/hm². Above all, covering plastic film in young apple-soybean intercropping system, combined with irrigation amount of 150 m³/hm² at branching stage, 400 m³/hm² at podding stage and 300 m³/hm² at grain filling stage could significantly increase the water use level and economic benefits in the intercropping system.