In order to reveal the pattern of variation and ecological adaptation of leaf morphological traits in the natural populations of Caragana microphylla, we collected leaves from ten natural populations of C. microphylla. We analyzed seven leaf morphological traits by multiple comparisons, nested analysis of variance, correlation analysis, cluster analysis and principal component analysis (PCA). The results showed that: (1) extremely significant (P < 0.01) variations of leaf morphological traits of C. microphylla were found within and among populations. The mean coefficient of variation (CV) was 10.13%, ranged from 6.23% to 12.78%. The mean phenotypic differentiation coefficient for all morphological traits was 43.62%, and the variation within population (30.09%) was higher than that among populations (24.91%), indicating that the leaf morphological variation within population was the main source of leaf morphological variation in C. microphylla. (2) Environmental factors also affected the variation of leaf morphological traits of C. microphylla, especially along the altitudinal gradient. The PCA results indicated that leaflet width, petiole width and petiole length played dominant roles. The results of UPGMA clustering analyses showed that ten populations of C. microphylla could be divided into three groups and two groups on the basis of leaf morphological traits and environmental factors, respectively. The Mantel test showed there was no geographic continuity in the variation of leaf morphological traits in C. microphylla. Overall, these results provided critical information for the adaptive evolution and utilization of the important species.