Partitioning soil water balance (SWB) is an effective approach for deciphering the impacts of vegetation change on soil hydrological processes. Growing apple trees on the Loess Plateau, China, leads to a substantial deep soil water deficit, posing a serious threat to the sustainable development of apple production. However, the impact of deep-rooted apple trees on SWB remains poorly understood. In this study, we conducted a “Paired Plot” experiment to achieve this objective by decoupling SWB components using water stable isotopes, tritium, and soil water contents from deep soil cores (up to 25 m) under apple orchards with a stand age gradient of 8–23 years. The results showed that deep soil water storage under apple orchards was notably reduced compared to nearby farmland, showing a stand age-related pattern of deep soil water deficit (R2 = 0.91). By analyzing the changing patterns of SWB components, we found that the main factor driving this deficit is the water uptake process controlled by the deep root system. This process is triggered by the increased transpiration demand of apple trees and short-term water scarcity. These findings have implications for understanding soil water dynamics, sustainable agroforestry management, and soil water resources’ protection in this region and other similar water-limited areas.