Abstract: Using three kinds of Panax notoginseng seedlings as materials, the difference of agronomic traits and physiological characteristics during seedling stage were measured. The results showed that the length and width of leaves, height, stem thick of the purple stem of P. notoginseng were bigger than those of the green stem and transitional stem. The activities of POD and PAL in the purple stem were higher than those of the green and transitional stem, while the content of chlorophyll was not significantly different among different color stems, the content of MDA in purple stem was lower than that of the green stem and transitional stem. Purple stem P. notoginseng had big leaf area, tall stout of agronomic advantage compared with the green stem and transitional stem, the stress resistance and potential of synthesis secondary metabolites of purple stem P. notoginseng were higher than that of the green stem and transitional stem.