We studied ion distribution in roots and the growth of Cyclocarya paliurus seedlings of three provenances, Huangshan in Anhui, Jiujiang in Jiangxi and Kunming in Yunnan, under conditions of 0, 1, 3 and 5 g/L NaCl stress using X-ray microanalysis. Results show that under NaCl stress of 3 and 5 g/L, the relative contents of Na+ and Cl- in root tissues increased, while the relative contents of K+, Ca2+ and Mg2+ decreased. With an increase in salinity, the relative content of Na+ in the epidermis and cortex of the root increased, while the relative content of Cl- in the stele and cortex of the root increased markedly. Thus, ions in the root tissues were unbalanced and the ratios K+/Na+ and Ca2+/Na+ decreased, while Na+/(K++ Na++Ca2++Mg2+) increased. The decrease of the K+/Na+ ratio and the substantial increase of Cl- in root tissues contributed to a decline in seedlings survival and reduced the increments for seedling leaf area, height, basal diameter as well biomass. Our preliminary conclusion is that the level of salt tolerance for the tested provenance seedlings was in the order of Huangshan > Kunming > Jiujiang, and the threshold of salt tolerance for C. paliurus seedlings was about 1 g/L.