Natural black and yellow quinoa varieties were used as experimental materials to study the effects of different salinity and alkalinity concentrations on the growth, antioxidant system and osmotic ion adjustment, the aim of which is to compare the tolerance of natural quinoa varieties to salt-alkali stress. The results showed that Salt-alkali stress promoted the root growth of two quinoa cultivars, but significantly inhibited the growth of stems and leaves, and the inhibitory effect exhibited higher for the black quinoa variety than for the yellow one. The CAT activity of the yellow quinoa variety increased damatically under high Salt-alkali concentration treatment, and its total antioxidant capacities (T-AOC) under different treatments were much higher than those of the black one, showing stronger scavenging ability of reactive oxygen of yellow quinoa variety. The ion selective absorption ratio (K+/Na+) were significantly different between before and after salt-alkali treatment. Before salt-alkali treatment, K⁺/Na⁺ of the black quinoa was higher than that of the yellow one; while after salt-alkali treatment, the K⁺/Na⁺ of the difference between the two quinoa varieties was gradually narrowed. Totally, K⁺/Na⁺ of the yellow quinoa variety was significantly higher than that of the black one under the high salt-alkali treatments, indicating the former was more resistant to salt-alkali stress than the latter. In conclusion, yellow quinoa is more salt-resistant and more suitable for cultivating in coastal salt-alkali soils.