Land use change can significantly affect soil hydrology in arid and semi-arid regions, making it crucial to understand the relationship between vegetation roots and soil moisture. Current models often fail to predict root growth and its impacts on water dynamics accurately. Our work presents a novel model that seamlessly integrates the Community Land Model (CLM) with the Soil & Water Assessment Tool (SWAT). Furthermore, it enhances the root module within the CLM, enabling more accurate simulations of dynamic root depth and distribution across varying tree ages. This improvement particularly considers the crucial processes of dormancy and plant maturity. Soil moisture and root patterns under apple trees of varying ages and in wheat fields on the Loess Plateau was analyzed. Our findings indicate that our dynamic root depth model outperforms traditional static models, and can accurately reflect soil moisture levels with high precision (R2 = 0.80–0.81; Nash-Sutcliffe efficiency (NSE) = 0.65–0.75). In contrast to methods that utilize fixed root depths, dynamic root simulation can provide new insights. As apple orchards mature, the roots of 22-year-old apple trees have been found to reach a depth of 21 m in the soil. Conversely, the maximum root depth of wheat is limited to 1.9 m. This latter finding aligns more closely with the measured root depths, highlighting the accuracy of dynamic simulations. This model reveals that older apple orchards show decreased soil moisture at greater depths (>20 m), contrasting with wheat fields that affect moisture mostly within the top 2 m. Our results underscore the crucial role of dynamic modeling in comprehending root-soil water interactions. Furthermore, they imply that extended orchard cultivation practices can lead to a substantial depletion of deep soil moisture. Specifically, over a period of 1 to 22 years, a water deficit of up to 85 mm yr−1 has been observed. For a 22-year-old forest, the D-D (dynamic distributions of coarse and fine roots) method calculates a significant cumulative deep Soil Water Storage loss. Over the course of 22 years, this loss amounts to 1664 mm, which is almost three times compare to the annual rainfall recorded. Such a large loss has the potential to significant impact on groundwater recharge. This highlights the need for careful consideration in future afforestation efforts to prevent increased soil aridity.