To explore the influence of water stress on fruit quality and gene expression related to citrate metabolism of ponkan. The test were conducted from May 15 to December 24 in 2013 using six-year-old ponkan (C. blanco cv. Ponkan) trees with 40% soil water conditions by taken regular watering as control. The content of acids in fruit were determined by HPLC, and relative expression of related genes of citric acid metabolic were determined by relative fluorescence quantitative PCR. The results showed that the content of citric acid, malic acid, quinic acid and total organic acids per gram sarcocarp were extremely increased by 285.2%, 320%, 480% and 299.1%, and the content of per-fruit organic acid were 77.39%, 89.64%, 117.24% and 75.9% respectively compared to those control in the fruit mature stage. Relative expression of CitCS1, CitCS2 were higher than control, and relative expression of CitAco1, CitAco2, CitAco3 had a certain increase in the late fruit development, were lower in mature stage. Three relative expression of CitIDH gene were higher than control in mature stage. Low CitGAD4 relative expression and undetectable in mature stage, the relative expression of CitGAD5 gene had a role in promoting under water stress. Furthermore, the relative expression of CitCS1, CitCS2, CitACO1, CitACO3, CitIDH1, CitIDH2, CitIDH3, CitGAD4 and CitGAD5 were influenced by water stress through the correlation analysis. Water stress caused the accumulation of citric acid, declined fruit quality, leaded to change of the genetic relative expression about citric acid synthesis and degradation. The down-regulation of CitACO1, Cit-GAD4 and up-regulation of CitCS1, CitCS2 might be one of the reasons that promoted to the accumulation of citric acid.