Abstract: This paper uses GIS and indicator Kriging method to analyze the spatial variability of soil total salinity, burial depth of phreatic water level and phreatic salinity before spring irrigation in Qingtongxia Irrigation Area at depths of 0～20, 20～40 and 40～60 cm, and satisfy the probability distribution map of certain threshold conditions, and the relationship between them is judged. The result shows:（1） The coefficients of variation of total soil salinity, burial depth of phreatic water level, and phreatic salinity in Qingtongxia Irrigation Area are all more than 1, which belongs to strong variation; the frequency distribution shows an obvious “high-top” phenomenon.（2） The indicated semi-variance function of soil total salinity at different depths and thresholds in Qingtongxia Irrigation Area conforms to different types such as spherical model, exponential model and Gaussian model. The indicated semi-variance function of the burial depth of the phreatic water level conforms to the exponential model. When the salinity thresholds are 1.0 and 2.0 g/L, the semi-variance function conforms to the exponential model, and when the thresholds are 2.5 and 3.0 g/L, the semi-variance function conforms to the Gaussian model. The soil total salinity and the burial depth of the phreatic water table under different threshold conditions show moderate-strong spatial autocorrelation, and the phreatic salinity shows a strong spatial autocorrelation.（3） The areas with high probability of mild, moderate and severe salinization and salinization of soil at the depth of 0～20 cm in Qingtongxia irrigation area account for 92.38%, 73.71%, 51.83% and 24.61% of the irrigation area. 20～40cm depth ratio is 92.15%, 50.21%, 6.87%, 0.53%; 40～60 cm depth ratio is 89.16%, 43.06%, 6.09%, 0.46%. When the depth of phreatic water thresholds are 1.5, 2.0, 2.5 and 3.0 m, the high probability areas account for 13.42%, 30.25%, 41.87% and 65.18% of the irrigation area. The high probability area accounts for 59.13%, 55.22%, 33.76% and 31.96% of the irrigated area when the phreatic salinity thresholds are 1.0, 2.0, 2.5 and 3.0 g/L. With the increase in the threshold, the area of high probability areas is significantly smaller.（4） When the soil in Qingtongxia Irrigation Area is moderately and severely salinized, the depth of phreatic water is 2.0 m, and the phreatic salinity is 2.0 g/L respectively. The comprehensive indicator probability distribution map and probability risk assessment obtained from the research have a guiding significance for the prevention and control of soil salinization in Qingtongxia Irrigation District, and can provide a reference for the high-quality protection and utilization of land resources.