This study was conducted to find out soil salinity spatial distribution and variation characteristics of Kongque River basin, and in turn to provide scientific basis for the amelioration and utilization of saline soil. Soil samples in each layer from 25 profiles were collected to determine the salinity of the soil. The spatial variation characteristics of soil salinity were investigated with the methods of geostatictics, and then the map of soil salinity spatial distribution was made. The results showed that the soils from 0–20 cm and 20–60 cm layers are in a moderate salinization and these from 60–100 cm layer are in a mild salinization. The soil salinity of each layer exhibited great spatial variation. The nugget-to-sill ratios are smaller than 25%, so the spatial correlations are strong. The spatial variation of soil salinity was mainly determined by structural factors. The soil salinity showed obvious spatial distribution regularity. In the horizontal direction, soil salinity increased firstly and than decreased from the upper river to the lower reaches. The salinization also increased with the increasing distance from the river. In the vertical direction, soil salinity decreased with the increasing depth of the soil profiles.