Taking phenotypic variation of Nitraria sibirica Pall.in 5 natural populations form Qinghai Plateau as objective,the variance analysis，correlation analysis，principal component analysis and cluster analysis of 8 phenotypic traits in 5 natural populations of Nitraria sibirica Pall. were studied.The relationship between phenotypic variation of the natural population and different distribution areas were discussed.The results showed that there was significant difference in morphologic chatacteristics between the populations，the variation between the populations was mainly due to the phenotypic variation.The correlation analysis between the phenotypic traits of Nitraria sibirica Pall.and geography factor showed that the mean annual precipitation was the most important factor that affected the morphologic characteristics，followed by the annual sunlight and the mean annual temperature.Principal component analysis showed that the main effect factors of phenotypic traits were coefficient of fruit shape，coefficient of seed shape，drupe number per fruiting-cyme and fresh fruit 100-fruit weight.Cluster analysis showed that five natural populations of Nitraria sibirica Pall.could be divided into 2 groups by SPSS cluster analysis.