Ginseng, a semi-shade perennial plant, is greatly affected by light. However, light quality has only been studied in a few papers involving growth tests under monochromatic light or based on hairy root cultures. A plant factory with light-emitting diodes (LEDs) may provide high precision and standardization of ginseng seedlings for transplanting, and plant responses to light quality should be investigated for designing the optimal lighting conditions for this environment. In this study, various ratios of red light (R):blue light (B) were set from 100:0 to 0:100% at the same photosynthetic photon flux density of 75 μmol m−2 s−1. As R increased, the shoot length became longer from R75B25, resulting in the single treatment of R being 1.68 times that of B. Compared to monochromatic R or B treatments, the overall growth of ginseng seedlings in R50B50 treatment increased. In the mesophyll structure, mixed light as R50B50 or while LEDs increased starch grains, and only R treatment led to dense chloroplasts in palisade and spongy parenchyma cells. Increasing R ratios had negative effects on CO2 assimilation rate (AN), light-saturated net photosynthesis rate (Asat), and chlorophyll parameters. The higher the R ratio, the higher the ginsenoside content in leaves, while roots were less affected by spectral changes. Monochromatic R induced malformation and senescence of ginseng leaves, while the addition of 25% B was sufficient to prevent the abnormal development of leaves and dysfunctional photosynthetic operation of ginseng seedlings. The results suggest that combinations of R and B should be considered when designing artificial lighting systems for a closed-type plant factory since R affects the morphological characteristics and ginsenoside content of ginseng seedlings.