Gibberellic acids had been proven to improve the fruit quality and storability by delaying deterioration and maintaining the antioxidant system. In this study, the effect of GA3spraying at different concentrations (10, 20, and 50 mg L−1) on the quality of on-tree preserved ‘Shixia’ longan was examined. Only 50 mg L−1GA3significantly delayed the decline of soluble solids (22.0% higher than the control) and resulted in higher total phenolics content (TPC), total flavonoid content (TFC), and phenylalanine ammonia-lyase activity in pulp at the later stages. The widely targeted metabolome analysis showed that the treatment reprogrammed secondary metabolites and up-regulated many tannins, phenolic acids, and lignans during the on-tree preservation. More importantly, the preharvest 50 mg L−1GA3spraying (at 85 and 95 days after flowering) led to significantly delayed pericarp browning and aril breakdown, as well as lower pericarp relative conductivity and mass loss at the later stages of room-temperature storage. The treatment also resulted in higher antioxidants in pulp (vitamin C, phenolics, and reduced glutathione) and pericarp (vitamin C, flavonoids, and phenolics). Therefore, preharvest 50 mg L−1GA3spraying is an effective method for maintaining the quality and up-regulating antioxidants of longan fruit during both on-tree preservation and room-temperature storage.