Soil water status and its resistance to evaporation differed seasonally, which is critical for ecosystem sustainability in arid areas. However, soil moisture content (SMC) alone fails to elucidate the distinctions in driving processes between seasons. The SMC, water stable isotope (delta 2H and delta 18O), and derived deuterium excess (dexcess) for different soil layers were investigated in the rainy and dry seasons in the upstream of the Yangtze River, Southwest China. The Delta SMC and Delta d-excess, defined as the differences in SMC and d-excess, respectively, between topsoil and subsoil, were proposed to reveal the contrasting governors of soil water between rainy and dry seasons. In the dry season, a significant relationship (R2 = 0.80, P = 0.040) between SMC and d-excess was found for the subsoil, while not in the rainy season. This suggested soil water status was governed by fractionated processes during long-term dry in the dry season while non-fractionated processes during the temporary dry period in the rainy season. Significant nonlinear relationships between Delta d-excess and Delta SMC were found in the rainy season (R2 = 0.83, P = 0.032) and the dry season (R2 = 0.96, P = 0.003), implying it can be used to identify differences in soil water driving processes. This nonlinear relationship also implies that the processes that driving recharge, water retention, and evaporation resistance are complex and interactive. Furthermore, these findings indicated that the topsoil (10 cm) largely mitigated evaporation-induced soil moisture depletion, albeit differently at different sites. Overall, integrating SMC, stable isotopes provides insights into the drivers of soil moisture.