Converting farmland to forest and grassland alleviated water loss and soil erosion. However, water-intensive grasslands and woodlands could form dry soil layers in the arid or semi-arid zones. Therefore, it is necessary to explore a management method to solve this pedological problem. In this study, based on the Environment Policy Integrated Climate (EPIC) model, the crop productivity and soil dry layer was predicted from 2018 to 2038 in alfalfa and apple land. Then, conservation agriculture and conventional tillage systems were used to repair the soil dry layer in apple and alfalfa systems from 2039–2050 in order to explore their potential. Model verification showed that EPIC simulations of yield, ET, and SWC were generally reliable. The predicted results showed that soil drought was more intense in alfalfa systems. Alfalfa’s annual decrease rate and total amount in the soil available water (SAW) were 27.31 mm year−1 and 652.76 mm, higher than 13.62 mm year−1 and 476 mm of the apple system, and the DSLT of apple’s system was thicker, but DSL-SWC was higher than alfalfa. In the recovery process, the restoration degree of soil desiccation in conservation agriculture was significantly higher than in conventional tillage systems (p < 0.05). In addition, the recovery effect increased with the increase of planting times of shallow root crops, such as potato and soybean. The recovery rate was 27.1 ± 1.72 mm year−1, DSLT was 750 ± 51.2 cm in conventional tillage systems, and the recovery rate was 44.7 ± 1.99 mm year−1, DSLT was 258.3 ± 74.9 cm in conservation agriculture systems. This study provides an effective farmland management method to alleviate soil desiccation and further reveals the new role of the Epic Model in future drought assessment.