Abstract:Codonopsis pilosula (Franch.) Nannf. (WE) and Codonopsis pilosula var. modesta (Nannf.) L.T.Shen (WN) are two major medicinal germplasms widely cultivated in Gansu Province, China. Based on a distant hybridization breeding strategy, two Codonopsis pilosula varieties and their 127 F1 hybrid individuals were used as experimental materials. Under indoor hydroponic conditions, 13 morphological traits of roots, stems, and leaves, as well as root lobetyolin content, were systematically measured and subjected to correlation analysis. The results showed that although no significant differences were detected in the mean values of most individual traits between the two parental lines, the WN population exhibited a higher Shannon diversity index (mean 1.297) than the WE population (mean 1.018), with average coefficients of variation of 72.85% and 72.21%, respectively. Moreover, the two populations displayed a tendency toward population differentiation in principal component distribution patterns and trait integration relationships. The F1 population showed the highest Shannon index (mean 1.56) but the lowest CV (47.57%), indicating a more even trait distribution with reduced amplitude of variation. PCA and clustering further demonstrated the formation of novel trait combinations in the F1 population. Most aboveground traits displayed significant mid-parent and over-parent heterosis with positive transgressive segregation. Lobetyolin content showed weak correlations with morphological traits in the parental populations but was significantly positively correlated with root diameter (r = 0.58, P < 0.01), root number, and root length in the F1 population. The results revealed limited morphological differences between WN and WE, while their hybrid progenies exhibited abundant phenotypic variation, thereby providing a theoretical basis for germplasm innovation and the selection of superior traits in Codonopsis pilosula.