By use of 18 provenances as the experimental material, we investigated the genetic variation of different agronomic characters and medicinal active ingredient content of Polygonatum cyrtonema Hua at the provenance level. The results showed that: 1) Except for the length of rhizome, all other agronomic characters including the height, ground diameter and polysacchride content were highly different at the provenance level; 2) The height, ground diameter, leaf area had positive correlation with the length, width, fresh weight of rhizome, while, the polysacchride content showed negative correlation with height, ground diameter, and width of rhizome, and the different provenances showed no obvious geographical variation; 3) Except for the height, the genetic variance of all other agronomic characters were lower than the environmental variance, with the genetic variation coefficients of the agronomic characters lower than the environmental variation coefficients; 4) Only both height and polysacchride content were in moderate to higher genetic controlled; 5) Five superior provenances of Hupingshan, Huochang, Xianxi, Dizhuang and Xianfeng were selected by using membership function method.