Desert halophytes are the plant groups which are widely distributed in Ebinur Lake Wetland. Under their influence, the change features of soil nutrient and salinity are of important significance to researching the mechanism that halophytes adapt to salinization environment. Based on the field survey on 3 different habitats (shrub habitat, meadow habitat, sparse arbor habitat) in Ebinur Lake Wetland in 2012 and 2013, elementary exploration was carried out on soil nutrient and salinity by using traditional statistical method and geostatistic method. The results showed that: (1) soil nutrient and salinity had significant elevated with increasing of the altitude and the distance from the lake under three different types of habitats. (2) the salt and nutrient accumulation in topsoil at the depth of 0~5cm were extremely significant, and the hierarchy was formed with higher high and lower low. (3)The soil organic matter, total nitrogen and total salt had the significant spatial structure feature and the uneven spatial distribution. The reason mainly lied in the micro topography, Fluctuation in Ebinur Lake Area, Parent material and climate changes and so on and distribution in the form of Strip and Patch; And (4) the regression analysis of the nutrition and salt in three different environmental soils displayed that, on the one hand, the variability of soil organic carbon was the key factor for the influence of soil total nitrogen,on the other hand, to some degree, the variability of soil salt was the important factor to effect the soil organic matter and soil total nitrogen.