The anatomical structure and nutrient content of three genotypes of walnut seedlings under salt stress were studied to reveal the response and adaptation mechanisms of salt stress and the differences in salt tolerance of different varieties. The annual seedlings of Northern California black walnut (Juglans hindsii)(J1), 'Zhongningyi’ (Juglans major×Juglans regia)(J2), 'Xinxin No.2’ (Juglans regia)(J3) were used as materials. The annual seedlings were treated with salt stress (0, 50, 100, 200 mmol/L NaCl) under pot conditions to study the microanatomical parameters of leaves and roots, and the changes of Na, K, Ca, Mg, Fe, Cu, Zn contents and their absorption, transportation and distribution characteristics in roots and leaves. The results show that: under salt stress, the thickness of leaves, upper epidermis, lower epidermis, palisade tissue, sponge tissue and root cortex, as well as the diameter of the root vascular bundle decreased in J1. The thickness of leaves, upper epidermis, lower epidermis, palisade tissue, sponge tissue and root cortex, the ratio of palisade tissue thickness to spongy tissue thickness, tissue tightness, diameter of root vascular bundle and root vessel, and the ratio of root cortex thickness to root diameter of J2 increased first and then decreased with the increase of salt concentration. Under salt stress, the thickness of leaves, lower epidermis, palisade tissue, the ratio of palisade tissue thickness to spongy tissue thickness, and the ratio of root cortex thickness to root diameter of J3 decreased. With the increase of salt concentration, the Na content showed an upward trend, which increased significantly at 200 mmol/L, and the Na content in J1, J2 and J3 leaves increased by 412.00%, 130.05% and 577.08% compared with the control. The absorption, transportation and distribution characteristics in roots and leaves of K, Ca, Mg, Fe, Cu and Zn were affected by salt stress, and K/Na, Ca/Na and Mg/Na decreased under salt stress, among which the decrease of Na/K and Mg/Na in J2 leaves was the smallest. The nutrient transport capacity of J1 was higher than that of J1 and J3. Walnut seedlings maintained the basic structure and function of leaves to resist salt stress by strengthening the selective absorption and transportation capacity of K, Ca and Mg by root transduction tissues. Combined with principal component analysis and membership function, the salt tolerance was in the order of hybrid walnut 'Zhongningyi’(Juglans major×Juglans regia) > 'Xinxin No. 2’ (Juglans regia) > Northern California black walnut (Juglans hindsii).