Nanotechnology has shown great potential to improve agricultural production and increase crop tolerance to abiotic stresses, including saline-alkaline environments. This study focuses on the biological mechanism of biocompatible iron-doped carbon dots (Fe-C-dots) nanozyme biosynthesized from artemisinin extract to alleviate saline-alkaline stress in wheat (Triticum aestivum L.). Particularly, Fe-C-dots with two types of natural enzyme mimicking properties, target reactive oxygen species (ROS) to assuage oxidative damage and to enhance the antioxidant capacity of enzyme-activated systems. Exogenous application of Fe-C-dots (50 mg/L) significantly promoted wheat growth and increased photosynthetic pigment content and photosynthetic efficiency. At the molecular level, Fe-C-dots treatment activated the nitrogen metabolism pathway of roots, up-regulated the expression of related genes OsNRT2.1, OsGS1, and NADH-GOGAT, and promoted the accumulation of nitrogen in wheat. Transcriptomics and metabolomics analyses reveal that Fe-C-dots triggered metabolic and transcriptional reprogramming in wheat seedlings. Besides, Fe-C-dots activated stress signaling and defense-related pathways, such as plant hormone signal transduction, MAPK, and photosynthesis signaling pathways, the cutin, suberin, wax, flavonoids, and phenolic acids biosynthesis. Importantly, compared to the control group, the application of Fe-C-dots under saline-alkaline stress increased the net photosynthetic rate (Pn) and transpiration rate (Tr) in wheat shoots by 77.5 %, and 78.6 %, respectively. These findings suggested that Fe-C-dots can improve root nitrogen metabolism and stem photosynthesis of wheat, as well as the synthesis of related stress-resistant compounds to cope with the damage of saline-alkaline stress on wheat growth. However, further studies are needed to explore the effectiveness of Fe-C-dots in wheat yield and quality evaluation.