In order to investigate the spatio-temporal variability of soil water content to rainfall under Caragana microphylla shrub in Horqin Sandy Land, a plot of 25 m × 25 m, where there were 6 shrub canopies of C. microphylla, was sited for measuring soil water content at two soil layers of 0-20 cm (top layer) and 20-40 cm (lower layer). Soil water content was measured on the 1st, 5th, 10th and 15th day after a 42 mm rainfall in Naiman of Inner Mongolia. The results showed that soil water contents at both layers under C. microphylla shrub were gradually decreased after the rain. Soil water content at the top layer out-side the shrub canopy was higher than that inside the shrub canopy within 5 days, and became similar inside and outside the shrub canopy on the 10th day after the 42 mm rainfall, and it was lower outside than that inside the shrub canopy on the 15th day. The soil water content at lower layer in the area without shrubs was higher than that under shrub canopy all along. All the measured values of soil water content can be fitted to a variogram model. There was significant autocorrelation of the values of soil water content between top layer and lower layer, except for the fourth measured values of soil water content at top layer. The range and spatial dependence of soil water content at top layer were lower than that at lower layer.