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Climate change has led to sea level rise and the salinization of arable land in coastal areas, which has affected the production of crops. Chenopodium formosanum Koidz. (djulis) has high nutritional value in Taiwan; however, the salt tolerance mechanism of djulis remains unclear. Therefore, the physiological salt tolerance mechanism of djulis was investigated in this study, which found that after the djulis sprouts were treated with 400 mM NaCl for 5 d, their growth was inhibited; the survival rate decreased by 45%, and the plant height and dry weight decreased by 9% and 36%, respectively. The content of the superoxide anion reactive oxygen species decreased as the treatment duration increased, whereas the H2O2 content increased with the treatment duration. The activity of antioxidants, namely ascorbate peroxidase, catalase, glutathione reductase, and superoxide dismutase, gradually increased as the treatment duration increased; the ratios of ascorbic acid to docosahexaenoic acid and glutathione to oxidized glutathione also increased significantly. The content of proline increased with the treatment duration. Moreover, the K+ content increased as Na+ accumulated. Accordingly, this study determined 400 mM to be the NaCl threshold level for djulis. Under the salt stress at this NaCl level, the djulis transported Na+ from the roots to aboveground portion and stored it in salt bladders to alleviate the toxic damage of Na+. In addition, proline and K+ were accumulated to adjust the osmotic pressure of cells.