Effects of low molecular weight chitosan (CTS) on drought resistance of the Red Fuji apple seedlings under water stress were studied using pot-culture experiments. The results showed that the treatment with CTS (20, 50, 100,150, 200 mg/L) could improve membrane stability, maintain or enhance the activities of SOD and CAT, and increase the content of soluble sugar under moderate water stress. The effects of CTS on drought resistance of apple seedlings may be related to concentration. The effect would be improved when the CTS concentration increased within a certain range. The best concentration was 100 mg/L, compared with CK2. The permeability of membrane and MDA content decreased by 29.89% and 75.56% (p < 0.05). The activities of SOD and CAT and content of soluble sugar increased by79.31% ,63.88% and 73.85% (p <0.05). If CTS concentration continued to increase, the effect of CTS on drought resistance would not enhance. Therefore, the mechanism of low molecular weight CTS of appropriate concentration that enhanced drought resistance may scavenge active oxygen species, protect membrane stability, maintain or increase the activities of SOD and CAT, increase accumulation of organic substance. Thus this mechanism might be the theoretical basis for application and research of CTS in adverse resistance.