[Objective] We conducted a field experiment to investigate the effects of intercropping green manure crops and their combination with ground fabric mulching on soil moisture, fertility, and apple yield. [Methods] Main treatments including intercropping ryegrass (NGR), oilseed rape (NGO), and alfalfa (NGA), sub-treatments including combined these with mulching ground fabric under trees (GR/GO/GA), and the control treatment is traditional clean tillage (CK) were designed. Additionally, 15N microplots were set up within main and control treatments. The responses of soil moisture, nutrients, and fruit yield were explored under the apple-green manure intercropping system. [Results] All treatments reduced soil water content (SWC) in which the decreasing range of GR (1.7%) was the smallest, relative to CK. Soil water difference ratio (SWDR) in main treatments were all negative, in which NGR had the smallest absolute value (0.5%) and NGA had the biggest (4.7%). All treatments increased evapotranspiration (ET), in which the increasing range of GR (0.3%) was the smallest, relative to CK. All treatments reduced the soil nitrate nitrogen (SNN) content, relative to CK. Compared to sub-treatments, the SNN and soil ammonium nitrogen (SAN) contents in main treatments averagely increased by 6.8% and 5.4%. Intercropping green manure (NGR, NGO, NGA) reduced 15N loss by an average of 56.4% (p < 0.05), relative to CK, with alfalfa showing the highest 15N utilization efficiency (39.4%) and ryegrass showing the lowest (19.7%). Compared to CK, ryegrass intercropping treatments (NGR, GR) increased SOM and TN contents by an average of 1.5% and 0.2%, respectively. In contrast, alfalfa (NGA, GA) intercropping treatments decreased by 15.2% and 15.4%, relative to CK. Ryegrass intercropping treatments (NGR, GR) showed the highest fruit yield and water use efficiency, with average increases of 12.1% in yield and 8.8% in water use efficiency, relative to CK (p < 0.05). [Conclusion] In conclusion, adopting the binary mulching pattern (ground fabric mulching under trees + ryegrass intercropping in inter-row) was beneficial to decreasing water consumption, nutrient loss, and increasing fruit yield and water use efficiency.