•Explored whether agroforestry is beneficial to the water relationship of plant.•Apple tree and corn compete for water sources at 40−80 cm.•WUE of vegetation in apple-corn combination were higher than that in monoculture.•40−80 cm should be sub-irrigated in the compound planting of apple tree and corn. Agroforestry of fruit tree-crops are widely used in the ecological construction of returning farmland to forestry in the Loess Plateau area, but disagreement persists over the water relationship between fruit tree and crops. To explore the rationality of fruit tree and crop intercropping, the stable isotopes were used to investigate the water sources of apple trees and corn in apple tree monoculture (A), corn monoculture (C) and apple-corn combination (AC), and the WUE of vegetation. The results indicated that the water source of apple tree was not significantly different between A and AC, though the utilization of water sources of corn in C was higher than that of AC. The layers of 60−80 cm (20.9–25.9 %) and 80−100 cm (22.8–24.7 %) were the major water source of the apple tree, while the corn also had two fixed water sources of 20−40 cm (18.8–33.1 %) and 40−60 cm (20.6–33.7 %) during the growth period. In addition, the apple tree mainly absorbed water from 40−60 cm (21.8–24.9 %) in the early and middle growth stages and from 100−200 cm (19.7–21.1 %) the in late growth stages. The corn predominantly used water from 0−20 cm (20.5–26.4 %) in the early growth stages and from 60−80 cm (17.2–42.5 %) in the middle and late growth stages. This indicates that there were competitions for water sources at 40−80 cm between apple tree and corn during the growth season. The water use efficiency (WUE) indicated that compound planting can improve the WUE of apple tree and corn. The WUE of corn in compound planting was 3.03–5.26 % higher than that of monoculture, though the WUE of apple trees in combination was higher than that of monoculture only when the soil water content was low. To achieve better ecological and economic benefits, 40−80 cm should be frequently sub-irrigated in the compound of apple tree and corn.