Take 20 wild Iris lactea germplasm materials collected from 11 leagues of Inner Mongolia as the research object, through the principal component analysis, correlation analysis and cluster analysis for the 13 agronomic traits, to discuss the genetic relationship between different germplasm, genetic variation characteristics and the reasons, and to provide theoretical basis for the development and utilization, resources protection and breeding of Iris lactea. The results showed that: (1) The agronomic traits of Iris lactea germplasm of different sources showed different degree of variability, and the variation coefficients range of 9.72%-300%, the traits with larger variation coefficients were 1000-grain weight, embryo length and germination rate, the traits with smaller variation coefficients were plant height and leaf width. (2) 10 main traits of 1000-grain weight, germination rate, water absorption, embryo length, endosperm length, seed length, reproductive shoot, vegetative shoot, leaf width and plant height were the major indexes which led to agronomic traits differentiation of Iris lactea germplasms of different sources. (3) There were different degree correlation among the agronomic traits, longitude, latitude and altitude were the main factors causing the variation of Iris lactea germplasm, embryo length, 1000-grain weight and water absorption were easily affected by environment factors. (4) 20 Iris lactea germplasm of different sources had been clustered into 4 classes, the vast majority of the germplasm materials showed obvious regionality, the regionality in similar longitude, latitude or habitat would be clustered into one class.