Abstract: In this study, we got a morphological dataset of leaf, flower and fruit of 46 populations including 827 individuals of Indigofera bungeana complex and conducted mean analysis, non-parametric test, multiple comparisons and principal component analysis using software SPSS 20.0. The results are as follows: Indigofera amblyantha is significantly different from the other species, while the morphological variation among I. bungeana, I. ramulosissima and I. silvestrii is not significant. The taxonomy of the four species need to be clarified with more evidence. The mean value of characters in southern China is larger than that in the Hengduan Mountains and northern China, which may be related to the phenotypic plasticity of the I. bungeana complex that we speculate. Comparing with the populations in the northern and southern China, populations in the Hengduan Mountains have high coefficient of variation and large morphological variation, which may be related to complex habitats in this region. The four species mainly differ in the length of the leaf, the petiole, and both the length and the width of the leaflet, and these characters can be used as the valuable taxonomic characters.