[Objective] The spatial-temporal patterns of soil water at the inter-dune area of Nitraria tangutorum nebkhas and its response to rainfall changes were determined in order to provide a scientific basis and data support for the accurate assessment of the role of inter-dunes in the soil water cycle and soil water stability in Nitraria tangutorum nebkhas. [Methods] The EM50 automated soil moisture measurement system was used to acquire long-term in-situ measurements of soil moisture in the clay layer of the inter-dune area. We analyzed the spatial patterns and temporal dynamics of soil water in the inter-dune soils under different rainfall conditions, quantifying the relationship between rainfall, soil water content before rainfall, and soil water infiltration and retention time in the inter-dune clay layer. [Results] ① From the perspective of the spatial variation characteristics of soil water in the clay layer, the variation degree of soil water in the 0-25 cm soil layer was characterized as moderate variation, among which the surface layer (0-15 cm) had greater variability and the lower layer (below 15 cm) had less variability. ② The magnitude of rainfall determined the infiltration depth and retention time of soil water at the inter-dune area after rainfall. As the average rainfall increased by 1 mm, the infiltration depth of soil water in the clay layer increased by 0.57 cm, and the soil water retention time increased by 1.05 days. Excessive soil water content before a rainfall event inhibited the continuous infiltration of soil water in the clay layer, but had a significant positive effect on soil water retention time after the rainfall, as shown by a 1% increase in soil water content before a rainfall event, and a 0.02 cm decrease in infiltration depth per unit rainfall, while the soil water retention time of the clay layer increased by 9.85 days. ③ Heavy rainfall events (＞20 mm) had an obvious replenishment effect on soil water in the clay layer, and the soil water decreased slowly after rainfall. [Conclusion] The inter-dune clay layer can inhibit soil water evaporation and provide good water storage and water retention.