The morphological variations of branches, leaves, flowers, fruits and seeds of Caragana microphylla and their correlations with environmental factors were analyzed based on five natural populations in the Xilingol steppe, Inner Mongolia, China. Nested variation analysis showed that there were significant differences in all of the 28 morphological characters within and among populations in 16 morphological characters, and the variations within populations were much greater than those among populations in most morphological characters. Cluster analysis showed that the five populations of C. microphylla could be divided into two groups in morphological characters, and there was significant positive correlation between the divergence of morphological characters matrix and geographical distance matrix. Principal component analysis showed that leaflet length, area of a compound leaf, fresh-mass of a compound leaf, and shoot fresh-mass were main morphological characters that varied among C. microphylla populations. Spearman correlation analysis showed that there were significant correlations between some morphological characters and soil factors. Soil N:P ratio, available N content, total N content, organic matter content and soil water content were main factors that were associated with morphological characters of C. microphylla.