Codonopsis pilosula （Franch.） Nannf. and Codonopsis pilosula var. modesta （Nannf.） L.T.Shen are two major medicinal germplasm widely cultivated in Gansu province， China. Based on distant hybridization breeding， 35 accessions of each parent along with 127 F₁ hybrid progenies derived from their cross were utilized as experimental materials. Thirteen morphological traits of roots， stems and leaves， along with the lobetyolin content in roots， were systematically measured and analyzed under indoor hydroponic conditions. The results demonstrated that the two parents exhibited no significant differences in the mean values of morphological traits， whereas C.pilosula showed a highly significantly higher lobetyolin content than C.pilosula var. modesta. However， the C.pilosula var. modesta population displayed a higher average genetic diversity index and average coefficient of variation than C.pilosula population. The F₁ population achieved the highest average genetic diversity index （1.56） compared to both parents， while its average coefficient of variation was lower than that of the parents， indicating a more stable phenotypic structure with reduced fluctuation amplitude. Principal component and hierarchical cluster analyses revealed that the F₁ population formed a novel trait combination structure. Most above-ground traits exhibited significant mid-parent and transgressive heterosis， presenting positive transgressive segregation. Lobetyolin content was weakly correlated with morphological traits within the parental populations. Crucially， within the F₁ population， lobetyolin content showed highly significant positive correlations with root diameter， number of lateral roots， and root length （P<0.01）. This study reveals that although the morphological differences between the two parental varieties are limited， their hybrid progenies display abundant phenotypic variation and structural reconfiguration between quality and morphological traits， providing a theoretical basis for germplasm innovation and indirect selection of superior agronomic traits in C.pilosula