Polygonatum kingianum is a characteristic and widely cultivated medicinal plant in Yunnan Province, and systematic evaluation of its germplasm resources is essential for elite line selection and genetic improvement. In this study, three systematically selected new lines (Yuxinhuang, Yuxinyan, and Yuxinhong) and one natural population were used as experimental materials. A total of 120 individual plants were analyzed, comprising 30 individuals randomly sampled from each of the four populations. Nine phenotypic traits and three quality traits were measured to systematically analyze genetic variation patterns and conduct a comprehensive evaluation The results indicated substantial genetic diversity among the tested materials. The coefficients of variation (CV) within lines and among lines ranged from 4.46% to 83.01% and from 8.03% to 77.35%, respectively. Notably, the variation in medicinal components was significantly greater than that in phenotypic traits. Correlation analysis revealed that plant height was extremely significantly and positively correlated with yield-related?traits. Furthermore, rhizome thickness was significantly positively correlated with polysaccharide content, and total peduncle length showed a significant positive correlation with saponin components, suggesting that aboveground morphological traits can serve as preliminary indicators of underground yield and quality traits. Principal component analysis (PCA) extracted four principal components with a cumulative contribution rate of 66.91%, screening out five core evaluation indices, including plant height and rhizome weight. Cluster analysis classified the 120 individual samples into four groups: Group I comprised high-yield materials, mainly represented by Yuxinhuang; Groups II and IV consisted of high-saponin materials, predominantly Yuxinyan; and Group III included high-polysaccharide materials, mainly Yuxinhong. Based on comprehensive scores derived from the membership function method, the top 30 elite individuals with superior overall performance were selected, including 15 Yuxinhuang, 13 Yuxinyan, and 2 Yuxinhong, while no accessions from natural populations were included. Overall, this study systematically elucidates the phenotypic and quality characteristics of different P. kingianum lines and highlights the comprehensive advantages of the Yuxin series elite lines, providing a solid theoretical basis and valuable germplasm resources for targeted breeding and efficient utilisation of P. kingianum.