In this study, a total of 14 morphological characters were investigated to reveal the genetic diversity in 78 accessions of Allium L. germplasms from Inner Mongolia in China. The results show that the Inner Mongolia Allium L. germplasms has abundant genetic diversity. The variation of average coefficient in 14 phenotypic traits was 43.0%, among them the number of flowers was the largest (94.7%) and seed thick was the smallest (14.6%). 14 phenotypic traits can be classified into six principal components, and the cumulative contribution rate was reached 80.77%, which could be reflected the phenotypic characteristics mostly among all of 78 accessions. A significant correlation was existed between the 14 phenotypic traits. The 78 accessions were divided into seven categories by using Euclidean distance system. This study reveals a higher genetic diversity existing in the Allium L.germplasms, provide a important implication for Allium L. germplasm characterization, improvement, and conservation.