Agricultural productivity is severely affected by soil salinity. In this study, seedlings of sunflower (Helianthus annuus L.) cultivar Baikuiza 6 were treated with Na‐based salts to induce salt stress or alkali stress. Salt had no effect on sunflower growth, while high concentrations of alkali significantly inhibited sunflower growth. The main characteristic for sunflower in response of salt or alkali stress was that it kept higher K+ concentration and lower Na+/K+ ratio, which is closely related to regulation of Na+ and K+ transport on cotyledon node zone (CNZ). The CNZ of sunflower restricted Na+ transport resulting in less Na+ in leaf than in root under both stresses, and it maintained relatively low Na+/K+ ratio in leaf and high selectivity for K+ vs. Na+. However, CNZ slightly restricted NO3− and H2PO4− transport under alkali stress compared with salt stress. This led to enhanced organic acid content to remedy the shortage of inorganic anions, and energy consumption is greater than for salt stress, which might be one cause of reductions of relative growth rate (RGR) under alkali stress.