Separation of water absorption by roots between trees and crops is critical to intercropping in water-limited regions. The current knowledge about interspecific water relationship is in one dimension, i.e., the vertical direction, little is known in both vertical and horizontal directions under different rainfall conditions. Therefore, an experiment was carried out in an apple tree based intercropping system and an apple tree monoculture on China's Loess Plateau during one growing season which started with a high rainfall period followed by a low rainfall period. We investigated the spatial distribution of soil water and plant root, and simulated their water use strategies using the 3D Hi-sAFe model. The root growth of apple trees in the top 60 cm was restricted by intercropping in the cropped area but increased in the top 40 cm in the uncropped area compared with monoculture. In the high rainfall period, compared with the control, the apple trees' water absorption from the uncropped area (0–60 cm) increased by 44.43%, but the water utilization from the cropped area (0–60 cm) decreased by 32.59%. More than 90% of the soil water absorbed by B. napus came from the 0–60 cm soil layer in the cropped area. During the low rainfall period, intercropping promoted an increase of 14.79% in apple trees' water absorption from the 60–100 cm soil layer in the cropped area. The soil water in the 20–60 cm layer became the main source for B. napus and its contribution was 63.51%, but only 20.56% of the water absorbed by apple trees came from here. It can be concluded that, to alleviate water competition, water absorption between species was segregated horizontally during the wet period due to the roots "niche differentiation", while water use complementarity occurred along the vertical axis during the dry period.