Astragalus membranaceus Bunge and Codonopsis lanceolata Benth. et Hook. f. are two medicinal species used to remedy inflammation, tumor, and obesity in Eastern medicine. Carbon dioxide (CO2) and supplemental lighting are two methods to enhance the growth, yield, and quality of crops. However, few studies have focused on the synergistic effects of CO2 and the supplemental light source on plug seedlings of medicinal species. In this study, uniform seedlings were grown with no supplemental light (the control) or under one of three supplemental light sources [high pressure sodium (HPS), metal halide (MH), or mixed light-emitting diodes (LEDs)] combined with one of three levels of CO2 (350, 700, or 1050 μmol·mol−1). The supplemental light (100 μmol·m−2·s−1 photosynthetic photon flux density) and CO2 were provided simultaneously from 10:00 pm to 2:00 am every day. The results showed that the supplemental lighting (LEDs, MH, and HPS) greatly improved the seedling quality with greater dry weights (of the shoot, root, and leaf), stem diameter, leaf area, and Dickson’s quality index (DQI) than those of the control in both species. An enriched CO2 at 1050 μmol·mol−1 accelerated the growth and development of plug seedlings, evidenced by the increased root and leaf dry weights, stem diameter, and DQI compared to the those from the other two CO2 enrichment levels. Moreover, LEDs combined with 1050 μmol·mol−1 CO2 not only increased the contents of soluble sugars but also the starch content. However, an enriched CO2 at 700 μmol·mol−1 was more suitable for the accumulation of total phenols and flavonoids. Furthermore, LEDs combined with 700 or 1050 μmol·mol−1 CO2 increased the chlorophyll, quantum yield, and stomatal conductance at daytime and nighttime for A. membranaceus and C. lanceolata, respectively. In conclusion, the data suggest that LEDs combined with CO2 at 1050 μmol·mol−1 is recommended for enhancing the growth and development of plug seedlings of A. membranaceus and C. lanceolata.