Intercropping systems reduce ineffective evaporation between trees but also intensify interspecific competition and reduce productivity. To improve the water-use efficiency and the economic benefits of an intercropping system on the Loess Plateau, China, where rainfall is limited and evaporation intense, an apple–soybean intercropping system with micro-irrigation water control was adopted to analyze the soil water, root density, water-use efficiency, yield, and economic benefits of intercropping under different micro-irrigation methods. Subsurface seepage irrigation, bubbler irrigation, and drip irrigation under mulching were used with irrigation upper limit levels of three maximum irrigation levels [60% (W1), 75% (W2), and 90% (W3) of field capacity (FC)]. Rainwater harvesting from ridges and furrows (GL) without irrigation was the control. Bubbler irrigation increased the soil water content, optimized the vertical soil water distribution, and promoted root growth. Except for the control treatment (GL), the other micro-irrigation treatments increased with the irrigation amount, but the water-use efficiency decreased. Drip irrigation under mulch combined with W2 (75% Fc) irrigation could obtain the maximum intercropping yield, which was increased by 71.1% compared with the GL treatment. Drip irrigation under a mulch combined with W2 produced the maximum intercropping yield; the economic benefits were higher under drip irrigation with mulching combined with W1; and all three micro-irrigation methods combined with W2 improved the economic benefits by 52.1–115.5% compared to GL. Drip irrigation under mulching or bubbler irrigation combined with W2 should be used when there are sufficient water resources, but drip irrigation under a mulch combined with W1 when there is a water shortage.