This paper investigated the variation in 17 main morphological characteristics of 3 Amorpha fruticosa populations inhabiting three sites (Lhasa, Qushui and Maqu) of the Qinghai-Tibet Plateau. Our results showed that there were striking differences in some of the morphological characteristics within and among A. fruticosa populations when compared the average coefficients of variation in these morphological characteristics. The average coefficients of the variation of 17 main morphological characteristics across the three populations were 0.09-0.37, with the average coefficient of new branch length variation being largest. In addition, the average coefficient of population variation in the Lhasa site greater than that for the other two sites. Principal component analysis (PCA) indicated that the accumulated contribution of the first four principal components was 86.6%, but the contribution of the first principal component was 40.9%, suggesting that the first four principal components explained most of the variation in the morphological characteristics. New branch length, new branch diameter, old branch diameter, taproot diameter and total length of the second-order lateral root explained the majority of the variation in morphological characteristics of A. fruticosa populations. Correlation analysis also indicated that there were complicated relationships between main factors (soil organic carbon, total nitrogen and so on) in the rhizosphere and the above five morphological characteristics. New branch length, taproot diameter showed significant positive or negative correlations (P < 0. 05) with the contents of soil nutrients, and in particular the content of soil organic carbon, total nitrogen, total phosphorus were significantly and negatively correlated (P<0. 05) with the five morphological characteristics. In addition, our results showed some of the differences in the distribution frequency of the first-order and second-order lateral root lengths of A. fruticosa plants within and among populations. The distribution frequency of the first-order lateral root lengths(10-20 cm and 20-30 cm)was generally larger than that for the other first-order lateral root lengths in the three sites, and the distribution frequency of the second-order lateral root lengths (0-10 cm, 10-20 cm, 20-30 cm, 30-40 cm, ≥40 cm) showed a decline trend in the Lhasa and Maqu sites. Moreover, the distribution frequency of the first-order and second-order lateral root lengths (≥ 40 cm) in the Maqu population was significantly greater than that for the populations of the Lhasa and Qushui sites. This study reported in the first time the variation in the main morphological characteristics of A. fruticosa plants in the alpine regions, which may have important implications for the management of such alpine grasslands in China.