Deep soil water, defined here as the soil water below a certain depth and not recharged by precipitation in one growing season, plays a critical role in maintaining eco‐physiological functioning in thick‐vadose‐zone regions. However, science‐based evidence remains limited on how and the extent to which deep soil desiccation (DSD) affects the eco‐physiological features of apple trees. Here, we improve a process‐based model to disentangle trees' transpiration and photosynthesis responses to precipitation and DSD below 200 cm (DSD200) on the semiarid Loess Plateau. We defined four DSD200 scenarios: 60%–70% of field capacity (FC) as a control, 50%–60%, 40%–50%, and 30%–40% of FC representing mild (MID), moderate (MOD) and severe (SED) desiccation, respectively; and five precipitation scenarios: extremely dry (285.78 mm), dry (392 mm), normal (457.72 mm), wet (524.96 mm), and extremely wet years (630.44 mm). We found that the stomatal conductance, net photosynthetic rate and transpiration under MOD and SED decreased significantly (p < 0.05), independent of precipitation years, indicating clear stomatal limitation induced by DSD200. This phenomenon was greatly enhanced in extremely dry years, with these variables decreasing on average by 29%, 36%, and 37%, respectively. Furthermore, SED resulted in non‐stomatal limitation with a great decrease in electron transport rates (Jmax) and maximum carboxylation rates (VCmax). Jmax and VCmax decreased by 40% and 26%, respectively, on average, in extremely dry years. These findings indicate that the combination of severe meteorological drought and deep soil drought resulted in non‐stomatal limitation for the apple trees. Persistent non‐stomatal limitation may be an important mechanism causing tree mortality in semiarid loess regions.