Water deficit drip irrigation (WDDI) in citrus orchards was found has a positive effect on fruit quality, particularly enhancing the soluble sugar content during the late period of fruit growth. However, the underlying molecular mechanism remains unclear. In this study, four deficit irrigation levels of D-60%, D-45%, D-30%, and D-15% were set at fruit expansion stage (stage III) and maturation stage (stage IV), respectively, and a fully irrigated treatment was set as the control (CK). Combined analysis of metabolomics and transcriptomics was used to reveal the molecular mechanism of sugar accumulation changes under different water deficit (WD) treatments. The results showed that sugar metabolism was growth stage dependent: stage III is a key period of sucrose metabolism and synthesis, while for stage IV, the accumulation of glucose and fructose increased significantly. Importantly, III-D15% and IV-D30% treatments were identified as optimal strategies for enhancing sugar content of citrus fruits. WDDI during the late growth stages up-regulated the expression of sugar metabolism-related differential expression genes (DEGs), consequently increasing the content of sugar-related differential expression metabolites (DEMs), and ultimately enhancing sugar accumulation in citrus fruits. For III-D15% treatment, DEMs related to sugar metabolism were mainly enriched in ‘carbon metabolism’, with significant increases in Sucrose, ɑ-D-Glucose-6 P and ß-D-Fructose-6 P content observed. SPS showed significant up-regulation, wihle BGLU, GN, TPS11, TPPF and TPPJ were down-regulated. For IV-D30% treatment, most DEMs were significantly enriched in ‘Glycolysis/Gluconeogenesis’. Key DEMs (Sucrose, D-Glucose-6 P, ß-D-Fructose-6 P) and DEGs (SUS, SPS, BGLU, HXK) involved in the metabolism and synthesis of sucrose, fructose and glucose were significantly increased. This study sheds light on the molecular mechanisms of sugar accumulation in citrus fruit under appropriate WDDI, providing valuable guidance for high-quality fruit production.