Salt stress is a major constraint affecting crop productivity, and understanding plant metabolic responses is essential for improving tolerance. In this study, we examined the metabolic pathways of flavonoids in flax (Linum usitatissimum L.) roots using a salt-tolerant genotype (R40) and a salt-sensitive genotype (R24). Plants were subjected to 150 mmol L⁻¹ NaCl, and changes in metabolites were analyzed using a widely targeted metabolomics approach. A total of 732 metabolites were detected, including 332 that increased and 400 that decreased under salt stress. Among these, 163 flavonoids were further analyzed to explore their role in stress response. KEGG pathway analysis revealed significant changes in flavonoid-related pathways, with 9 pathways upregulated, 10 down-regulated, and 4 showing mixed responses. Key metabolites with strong antioxidant properties, such as quercetin and epicatechin, were identified as important components of the plant’s defense mechanism. Notably, clear differences were observed between the tolerant and sensitive genotypes in terms of flavonoid accumulation and metabolic patterns. These findings highlight the important role of flavonoids in helping flax cope with salinity stress and provide useful insights for developing salt-tolerant varieties.