In order to explore the salt tolerance mechanism of Machilus thunbergii, the effects of salt stress on seedling biomass, root morphology, sodium and potassium absorption and distribution were studied. The results showed that the above-ground biomass increased slightly under lower salt stress conditions, while the below-ground biomass, root length and root surface area showed a downtrend. The above-ground growth was limited under high concentration salt stress, while the under-ground growth was not subject to significant restrictions. The absorption of Na+ in root increased under salt stress, but that of K+ decreased. The ability of Na+ transporting from root to leaf and stem was weakened. The accumulation of Na+ in stem and leaves was less. With the decreased absorption of K+, the ratio of Na+/K+ also continuously increased. With the increased concentration of salt stress, the ability of K+ absorption in roots increased. The ability of K+ transporting from root to leaf and stem was enhanced, which resulted in significant increase of K+ in the leaves and stem. The accumulation of Na+ in the under-ground was significantly greater than that in above-ground, while the K+ content in above-ground increased significantly, which played a key role in maintaining normal growth and metabolism of M. thunbergii.