The changes in the concentrations of endogenous hormones and their influence on carbohydrate metabolism in leaves of micropropagated Fuji apple plants were studied under water deficiency stress. The results showed that water stress induced a rapid increase in the concentration of abscisic acid (ABA) and led to a decrease in concentrations of both zeatin and gibberellins (GAs). The concentration of indole-3-acetic acid (IAA) changed in an independent manner, which was not correlated with the different levels of water stress. With regard to the carbohydrates, the contents of sorbitol and sucrose increased, whereas the content of starch decreased. The increase in the concentration of ABA was significantly correlated with both the increase in the activity of aldose-6-phosphate reductase (A6PR) and the decrease in the activity of sorbitol dehydrogenase (SDH), indicating that ABA played a regulatory role in sorbitol metabolism. The concentration of ABA was positively correlated to the activity of sucrose-phosphate synthase (SPS) but negatively correlated to the activities of acid invertase (AI) and ADP-glucose-pyrophosphorylase (ADPGppase) in water-stressed plants, which indicated that ABA promoted sucrose synthesis and inhibited sucrose degradation and starch synthesis at the same time. Under conditions of water stress, the decrease in the level of zeatin was accompanied by a decrease in the activities of SDH and ADPGPPase. GAs concentration showed positive correlation with ADPGPPase activity. IAA showed no significant correlation with any of the enzymes tested in this study. The results of this study suggested that ABA might be one of the key factors regulating the distribution of carbohydrates under water stress. The metabolism of sorbitol and starch under conditions of water stress might be regulated by the combined action of many plant hormones.