The influence of water stress on fruit quality and gene expression related to citrate metabolism of citrus were conducted from July 5 to November 15 in 2012 using five-year-old satsuma mandarin trees with 40% soil water conditions by taken regular watering as control. The results showed that water stress significantly decreased single fruit weight, peel weight, fruit transverse and longitudinal diameter of citrus by 59.0%, 61.7%, 25.2% and 21.7% compared to the control, respectively. Water stress brought about the decrease of ascorbic acid and juice content in fruit, however, soluble solids was promoted. Furthermore, it was found that the content of sucrose, glucose, fructose and total sugar per gram sarcocarp in water stress were raised obviously by 33.3%, 72.3%, 65.0% and 48.9% respectively, the content of them in single fruit, while, were obviously declined by 42.1%, 25.1%, 28.3% and 37.8% respectively. The content of total organic acids and citric acid per gram sarcocarp were extremely increased by 66.3% and 60.4% respectively compared to those in the control. So did the content of citric acid and total organic acids per gram sarcocarp which were very significantly increased by 11.3% and 50.6% respectively. Related gene expression results indicated that the expression level of CitCS was increased while CitIDH degreased in water stress. CitACO was increased at the late stage of fruit growth. In general, water stress could obviously suppress the growth of satsuma mandarin and significantly caused the accumulation of citric acid as well as lead to the decrease of sugar content in fruit, which resulted in the decline of the ratio of sugar to acid and fruit quality. The up-regulation of CitCS and down-regulation of CitIDH might be one of the reasons that promoted to the accumulation of citric acid.