The statistical methods of cluster analysis and the Principal Component Analysis (PCA) were used to study 12 morphological characteristics from 12 populations of Medicago ruthenica in Inner Mongolia .The results show: the genetic diversity of 12 gemplasm is abundant, inter-population variation occurred remarkably in most morphological character except for pod shape, seed width. The first and second principal components totally represented 62.30% of morphological diversity, principal components analysis showed: five characters including Branch length ,area of leaf ,pod width ,seed length and 1000-seed weight are mainly factors which produced morphological variation of Medicago ruthenica .Based on the morphological data , 12 Medicago ruthenica germplasm were clustered into 4 groups. The first group, including MR-12 of germplasm, had taller plant height, more plant branches and leaves, bigger pod length, and more 1000-seed weight. The germplasm in cluster had better morphological trait, and it could be used for breeding.