Abstract: Ecological organic cultivation is an increasing trend in the industrialized development of traditional Chinese medicine. The medicinal properties of Codonopsis pilosula vary with seedling size. To explore the effects of seedling size on medicinal formation in organic cultivated C. pilosula, seedlings were categorized as big (BS), middle (MS), small (SS), and slender (SLS) seedlings and transplanted under full organic conditions to comparatively evaluate the yield and medicinal characteristics of the medicinal roots. The results showed that the seedling sizes had an allometric growth pattern. After transplantation, bigger seedlings showed earlier regreening, greater growth at the early stages and weaker growth at the later stages with significant increases in lateral roots number, and higher water content of roots, and higher disease incidence. The smaller seedlings showed later regreening, faster growth at the mid and later stages with increased diameter, less root water content and lower disease incidence. These differences led to non-significant differences in the single root weight and total medicinal yield. The average fresh medicinal yields of MS (8225.1 kg·hm^–2) and SS (8125.0 kg·hm^–2) were the highest and second highest, respectively, increasing by 23.4% and 21.9% compared with the BS group and by 45.2% and 43.4% compared with the SLS group. The average dry medicinal yield of SS (2938.1 kg·hm^–2) and MS (2681.1 kg·hm^–2) was the highest and second highest, increasing by 37.8% and 25.7% compared with the BS group and by 53.6% and 40.1% compared with the SLS group, respectively. Among the four seedling sizes, the root disease incidence did not significantly differ, ranked as BS (6.4%) > MS (5.6%) > SS (3.9%)> SLS (3.6%). However, the disease severity showed significant differences, and the disease indices for MS and BS were 4.66% and 2.93%, respectively, both of which were significantly higher than those for SLS (1.32%) and SS (0.97%). The comprehensive evaluation indices were SS (0.734) > SLS (0.636) > MS (0.409) > BS (0.282). In summary, yield did not increase with seedling size largening. Plant seedlings have strong plasticity and manifest various strategies for establishment during the medicinal formation period. These results challenge the traditional selection and retention practices for plant seedlings, suggesting that the big seedlings should not be blindly chosen and that the slender seedlings should not be eliminated during production. Slender plants should be cultivated by increasing the transplantation density and controlling pests and birds to improve the regreening rate, whereas larger seedlings should be cultivated by decreasing the density. Together, these practices could improve the effectiveness of C. pilosula organic cultivation.