The spatial distribution of soil salinity and the depth to groundwater are of great importance in guiding rational irrigation water use and controlling soil salinization. The secondary saline-alkalization problem of soil is quite severe in Hetao irrigation, Inner Mongolia due to increasing rise of groundwater table caused by unsuitable irrigation method and incomplete drainage system, in particular under the specific arid and semi-climatic and hydrogeological conditions. This has become one of the major constraints to local agricultural and social-economic development. In this paper, the Shahaoqu irrigation district was chosen as an example for testing the spatial variability of soil salinity and its relationship to depth to groundwater. Aiming at the complexity and spatial variability of the dynamic soil water and salinity in Shahaoqu irrigation district, the classical statistics and geostatistics integrated with GIS were used in this study to analyze the spatial variability of soil EC values in 0-20cm, 20-40cm and 40-60cm depths and the effect of the depth to groundwater on soil salinity distribution in Shahao irrigation area of Hetao irrigation district. The results showed that the soil EC's Cv values were all more than 36% in Shahao irrigation area and had strong spatial variability in different irrigation periods and different soil depths, Analysing the EC data with GS+ software, it was found that the spherical model, gaussian model and exponential model were perfect in fitting Semi-variogram of soil EC values, the soil EC data had moderate spatial correlation, and the spatial autocorrelation of soil EC values reached the highest in 0-20cm. After finishing the Kriging map of salt in three soil layer respectively, it was found that the spatial distribution of soil EC values was in a trend of increase from south to north in different soil depths before autumn irrigation, and the high soil EC values were in northwest or northeast areas after autumn irrigation. Soil salinity is significantly affected by the depth to groundwater in Hetao irrigation district, and the detpt to groundwater is a decisive factor affecting soil salization. From the Kriging map of the depth to groundwater, it was found that the depth to groundwater was deep in the south and shallow in the north, and it reached the deepest 2.71m on the average before autumn irrigation. However, the average depth to groundwater reached the shallowest 0.75m after autumn irrigation due to groundwater recharge from irrigation water. Soil salinity decreases with the increase of the depth to groundwater, they conform to exponential relations. In order to prevent the soil salinity from accumulating in the root layer, controlling the depth to groundwater is an important fractor for controlling soil salinization in Hetao irrigation district. Therefore, some reasonable irrigation measures and agriculture technology measures should be adopted to control the depth to groundwater, and thereby to prevent the aggravation of soil salinization in this irrigation area. This study could provide lots of scientific support for soil salinity treatment and improvement, agricultural planning and adjustment, and irrigation and drainage engineering planning in the future.