In citrus fruit, citric acid is the predominant organic acid which influence fruit taste, flavor and quality. The effect of hot air treatment (HAT 40°C, 48 h) and 1.0% chitosan coating on the change of organic acids and the related gene expression of citric acid synthesis and degradation in ponkan (Citrus reticulata Blanco) fruit during cold storage have been studied. The results showed that citric acid was the main organic acid in fruit, the trend change of citric acid content was consistent with total organic acids and titratable acidity (TA) content, which decreased with the prolongation of storage time, hot air treatment significantly promoted but chitosan coating treatment significantly delayed citric acid degradation in Ponkan fruit. Hot air treatment could induced CitAco2/3, CitIDH2/3, CitGAD4, CitACLs, CitPEPCKs and CitFBPases expression during fruit storage period, but had no significant effect on CitGSs expression, The enhanced expression of degradation-related genes was closely related to the degradation of citric acid. The expressions of CitAco3, CitGAD4 CitACLα2/β, CitPEPCKs and CitFBPases were inhibited, which leading to the degradation rate of citric acid was slowed by chitosan coating during storage. These results showed that the degradation of citric acid in fruit was regulated by ATP citrate lyase (ACL) pathway and γ-aminobutyric acid (GABA) pathway.