To systematically elucidate the growth response characteristics of pigeon pea（Cajanus cajan）seedlings under different concentrations of salt stress and the dynamic changes in antioxidant enzyme activities and flavonoid metabolite accumulation，uniformly grown pigeon pea seedlings were used as plant materials. The seedlings were treated with 0，50，100，150，and 200 mmol⋅L^-1 NaCl solution. Phenotypic observation and root scanning analysis were conducted at 1，3，5，and 7 days after treatment. Root morphological parameters，including root length，surface area，projected area，volume，and average diameter，were measured. Meanwhile，the activities of superoxide dismutase（SOD） and peroxidase（POD） were determined. In addition，samples collected under 150 mmol⋅L^-1 NaCl treatment at different time points were analyzed using UPLC-MS/MS for qualitative and quantitative profiling of flavonoid metabolites，combined with analysis of related gene expression changes. Results showed that salt stress significantly inhibited the growth of pigeon pea seedlings in a concentration-dependent manner. With increasing salt concentration and prolonged treatment duration，seedlings exhibited inhibited primary root elongation，restricted lateral root development，and reduced shoot growth，with the inhibitory effect becoming more pronounced after 3 days of treatment. Root morphological parameters generally increased over time；however，the magnitude of increase was significantly reduced under 100 mmol⋅L^-1 and higher NaCl treatments，whereas 50 mmol⋅L^-1 NaCl showed a promoting effect on root growth at certain time points. The average root diameter showed relatively small variation under 50 mmol⋅L^-1 NaCl treatment but slight increase under moderate to high salt conditions. SOD activity increased significantly under moderate salt concentration and then stabilized，while POD activity continuously increased with increasing salt concentration and treatment duration. Under 150 mmol⋅L^-1 NaCl treatment，flavonoid metabolites in roots exhibited stage-dependent accumulation patterns. Root stilbene acid mass concentration showed an overall increasing trend，isovitexin mass concentration fluctuated markedly，genistin displayed induced accumulation，and genistein mass concentration significantly increased at later stages of treatment. Gene expression analysis showed that the expression levels of CcPAL2，Cc4CL4，and CcCHS3 were downregulated，while CcC4H1 was significantly upregulated，and CcCHI2 and CcIFS1 were also induced. In conclusion，salt stress inhibited the growth of pigeon pea seedlings and showed clear time- and concentration-dependent effects. Antioxidant enzyme activities and flavonoid metabolite levels dynamically changed during the stress process，and the key genes in the flavonoid biosynthesis pathway exhibited differential regulation under salt stress conditions.