Cover crops between rows in orchards can improve the development of soil resources and increase agricultural productivity. However, there have been few reports of cover crops that can act as a “green manure” in apple orchards across arid and semiarid zones. This study investigated the effects of planting interrow vegetation on soil properties and apple tree performance during a 32-month experiment. There were six treatments: clean cultivation as a control; natural grass planting; planting with ryegrass; planting with alfalfa; planting with tall fescue; and planting with villous wild pea cover crops. The treatments primarily affected the 0- to 20-cm surface soil layer. Soil carbon, nitrogen, and enzyme levels initially decreased (during the first 12–24 months); then, they increased (24–32 months). The cover crops significantly increased nutrient contents (soluble organic carbon, microbial carbon and nitrogen, alkaline dissolved nitrogen, nitrate nitrogen, and ammonium nitrogen) in the 0- to 20-cm soil layer by more than 19.6% and increased the related enzyme activities by more than 25.2%. The alfalfa and wild pea alleys had a stronger effect on the soil environment than the control, natural grass, ryegrass, and tall fescue alley treatments; however, after 32 months, the alfalfa treatment inhibited fruit tree growth and development. This was unexpected because alfalfa seemed to have a positive effect on soil fertility characteristics. Under local ecological conditions, villous wild pea had the greatest effect on apple orchard productivity and significantly increased short branching by 15.9%, fruit weight per fruit by 12.6%, yield per plant by 8.6%, and soluble sugar content by 10.5% compared with clean cultivation. The correlation analysis showed that there were significant or highly significant positive correlations between fruit tree performance and soil carbon, nitrogen, and enzyme activity levels as the soil layer depth increased. Therefore, under local ecological conditions, cover crops have a greater effect on orchard surface soil fertility than on deeper soils, and intercropping with villous wild pea potentially produces the greatest improvement in apple orchard productivity.