The purpose of this study was to explore the phenotypic diversity of Gentiana rigescens Franch. ex Hemsl and establish a comprehensive evaluation method for excellent provenances of the species. The phenotypic datasets of 19 traits in 477 individuals from Yunnan Province were collected. The Shannon-Wiener diversity index, principal component analysis, membership function, and partial least square were used to evaluate the provenances of G. rigescens. The value of Shannon-Wiener diversity index (H'') of root, stem, and leaf traits of 477 individuals ranged from 1.59 to 2.06. At the several traits such as root diameter (H'' = 2.00), stem diameter (H'' = 2.00), root/biomass ratio (H'' = 2.02) and root water content (H'' = 2.06), the highest H'' values were observed. The dry weight of aerial part of plants showed the lowest (H'' = 1.59) H'' value. The plant traits of G. rigescens which was from different geographical regions were significant differences (P < 0.05). Notably, the root yield traits value of G. rigescens from southern Yunnan was significantly higher than those in other distribution areas (P < 0.05). Based on the comprehensive evaluation value (D value) of phenotypes, the D value of 477 G. rigescens ranged from 0.50 to 2.45. The individuals collected from western and northwestern Yunnan (D average = 1.17 ±0.03) and southern Yunnan (D average = 1.19 ±0.37) had higher comprehensive evaluation value. Meanwhile, the D value of the individuals collected from central Yunnan (D average = 1.00 ±0.30) and southeastern Yunnan (D average = 1.00 ±0.32) were lower. The Yunxian population had the highest comprehensive evaluation value of plant (D average = 1.24±0.14), and small differences in traits among individuals within the population (CV = 28.77%). It suggested that individuals of Yunxian population were excellent provenances. Through the analysis of PLS-R and PLS-DA, it was found that root fresh weight, root dry weight, dry weight of plant, branch number, fiber number, dry weight of aerial part, stem diameter and leaf length (VIP > 1.00) were the key traits for the discrimination of good and bad provenances. And the environmental factors such as soil properties, precipitation during plant growing period and average temperature in the driest season were closely related to the high yield traits of G. rigescens (VIP > 1.00). The higher content of sandy and the lower content of clay in soil, drought and high temperature might lead to reduce of root fresh weight, dry weight and root number. The higher precipitation in April, May and November was observed with positive effects at root-relates traits.