Iron is the most demanded trace element among the essential micronutrients for plants, participating in the electron transport chain processes such as cytochrome and ferredoxin in photosynthesis. Iron can activate enzymes like catalase and peroxidase, helping to eliminate free radicals and enhance the stress resistance of crops. In recent years, nano-iron powder has been widely applied in agricultural production, including in grains, oilseeds, and Chinese herbal medicines, with significant yield-increasing effects. However, there are no reports on the application of nano-iron in improving the salt and alkali tolerance of flax and its physiological mechanism. This study aimed to verify the effect of nano-iron on the growth traits of flax in saline-alkali soil through the analysis of growth traits and metabolic pathways, and to explore the mechanism of action of related metabolites in promoting salt tolerance in flax through statistical analysis. The results showed that,emergence rate, survival rate, root diameter and stem diameter of flax increased by 24.8%, 22.5%, 25.7% and 6.9%, respectively, in saline-alkali soil after nano-iron treatment. Through non-targeted metabolomics testing, 15 up-regulated metabolite types including amino acids and their derivatives, ketones, and lactones were screened out, and their information related to the salt tolerance of flax was obtained. By screening metabolic pathways and analyzing the salt tolerance mechanism, four pathways were selected from 20 metabolic pathways, and the metabolites related to salt tolerance were precisely screened out on each pathway. Among them, five metabolites, including arginine-threonine-lysine-arginine peptide, Histidine leucine, N-L-histidine L-leucine, Arginine-isoleucine-threonine-valine-lysine polypeptide and Na-ser-oh, were screened out on the amino acid metabolism pathway; two metabolites, PA and PC, were screened out on the lipid metabolism synthesis pathway; one metabolite, lupeol, was screened out on the sesquiterpene and triterpene biosynthesis pathway; one metabolite, 3,5-dihydroxydecanoate, was screened out on the alcohol biosynthesis pathway.