Soil salinization and low soil fertility are the key limiting factors for soil improvement in the Huanghuaihai Plain at present. To evaluate the spatial variation of soil salinization and fertility, we used GIS and indicator Kriging of nonparametric geostatistics to analyze the spatial distribution of soil salinity content and organic matter content in top 20cm soils for a typical county located in Huanghuaihai Plain, Yucheng City,northwest of Shandong province. The probability maps for soil salinity content and organic matter content that met the given thresholds(soil salinity threshold is 0.29 dS/m, organic matter threshold is 15 g/kg) were presented.The results indicated that the indicator Kriging method was able to produce stable semivariograms for both soil salinity content(greater than 0.29 dS/m) and organic matter content(less than 15 g/kg),which exhibited moderate spatial autocorrelation due to the combined effects of structural and stochastic factors in our study area. Both univariate indicator Kriging and multiple-variable indicator Kriging(soil salinity greater than 0.29 dS/m and organic matter less than 15 g/kg) interpolation maps showed that the probability distribution of soil salinity and organic matter was regular and similar in spatial variation. Specifically, high soil salinity content and low soil organic matter content occurred at northwest (Zhangzhuang Town), west (Fangsi Town) and south (Juzheng Town) of the study area, in which the soils to some degree suffered from secondary salinization risk. In addition, high soil salinity content and low soil organic matter content occurred at the high flood plain along the Tuhai river, the major high-yield region in the study area where the soil was classified as alluvial Cinnamon soil and suffered from low salinization risk. Since the integrative probability map as well as its risk assessments are significantly valuable to the management and sustainable use of soil resource, our results are of great use to the soil improvement in the study area.