Euhalophyte Salicornia europaea L., one of the most salt-tolerant plant species in the world, can tolerate more than 1000 mM NaCl. To study the salt tolerance mechanism of this plant, the effects of different NaCl concentrations on plant growth, as well as Na⁺ accumulation and distribution at organ, tissue, and subcellular levels, were investigated. Optimal growth and an improved photosynthetic rate were observed with the plant treated with 200–400 mM NaCl. The Na⁺ content in the shoots was considerably higher than that in the roots of S. europaea. The Na⁺ in S. europaea cells may act as an effective osmotic adjuster to maintain cell turgor, promoting photosynthetic competence and plant growth. The results from the SEM–X-ray and TEM–X-ray microanalyses demonstrate that Na⁺ was compartmentalized predominantly into the cell vacuoles of shoot endodermis tissues. Accordingly, the transcript amounts of SeNHX1, SeVHA-A, and SeVP1 increased significantly with increased NaCl concentration, suggesting their important roles in Na⁺ sequestration into the vacuoles. Therefore, a multiple sodium compartmentalization mechanism is proposed to enhance further the salt tolerance of S. europaea.