The low yield and active ingredient content of medicinal plants is always a challenge. Nanotechnology offers new tools for enhancing the biomass and metabolism of medicinal plant. In the present study, the effects of two nanomaterials (NMs) on the growth, photosynthesis, antioxidant system, mineral homeostasis, C/N accumulation and content of active ingredients of Isatis indigotica (BLG) were investigated. BLG was grown in soil supplemented with 10-250 mg/kg of multi walled carbon nanotubes (CNTs) or iron oxide nanoparticles (Fe2O3 NPs) for 60 days in a greenhouse. The results showed that low concentration (10 mg/kg) of Fe2O3 NPs promoted the growth of BLG, while the opposite trend was observed in CNTs treatment. Fe2O3 NPs at 10 mg/kg effectively increased the shoot length and biomass by 21 and 14%. Notably, the Fe2O3 NPs could also effectively enhance the officinal ingredient content of BLG by regulating the antioxidant system, mineral element homeostasis, and carbon and nitrogen synthesis. Fe2O3 NPs at 10 mg/kg increased the flavonoids, soluble sugars, and total protein content of BLG roots by 55%,124% and 59%, respectively. In conclusion, our results suggest that the Fe2O3 NPs can be used as a bio-fortifier to enhance the yield and officinal quality of BLG.