【Objective】This study aims to investigate the dynamic physiological and biochemical responses of Juglans regia ‘Robert Livermore’ seedlings to a combined saline-alkali stress, and to clarify the regulatory patterns of their saline-alkali tolerance capacity.【Method】Potted seedling control experiments were conducted using three concentration levels (100, 150 and 200 mmol/L) of a (NaCl+NaHCO₃) mixed solution as the stress treatment groups, with water as the control group (CK). On the 7th, 14th and 21st day after stress initiation, photosynthetic parameters, chlorophyll fluorescence characteristics, and various physiological indicators were measured. Furthermore, the expression levels of key genes in the anthocyanin biosynthesis pathway were determined, and the correlation between anthocyanin content and the expression of these key genes was analyzed using mantel-test statistics.【Result】With increasing stress concentration and duration, leaf margin curling and scorching intensified significantly, while relative growth in height (RGH), relative diameter growth (RDG), leaf relative water content (LRWC), and biomass all decreased markedly. Under short-term stress, photosynthetic capacity (net photosynthetic rate (Pn), transpiration rate (Tr), stomatal conductance (G_s)) declined rapidly. Under high saline-alkali conditions, the relative fluorescence intensities at points I and P on the OJIP curve increased significantly, accompanied by a decrease in electron transport efficiency (ABS/RC, TR_o/RC, ET_o/RC, DI_o/RC). In the later stages of stress, superoxide dismutase (SOD) and peroxidase (POD) activities continued to increase, leading to a declining trend in malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) contents. The contents of secondary metabolites, flavonoids and polyphenols, accumulated continuously with increasing stress intensity. Principal component analysis of physiological parameters indicated that under short-term stress, the clearance of excess reactive oxygen species (ROS) was facilitated by increased levels of secondary metabolites such as flavonoids, polyphenols, and anthocyanins. As stress duration extended, osmotic adjustment substances (soluble protein and proline) increased significantly.【Conclusion】Under combined NaCl and NaHCO₃ stress, the growth of J. regia ‘Robert Livermore’ seedlings was inhibited and photosynthetic efficiency declined. Short-term stress triggered enhanced antioxidant enzyme activity and accumulation of secondary metabolites to scavenge excess ROS, accompanied by upregulation of the JrAOMT gene promoting anthocyanin synthesis. Under the long-term stress, osmotic adjustment capacity was improved by regulating SP and Pro contents to maintain adaptability to the stressful environment.