In arid areas, water shortage has become a major bottleneck limiting the sustainable development of agriculture, necessitating improved water use efficiency and the full development of innovative water-saving irrigation management technologies to improve quality. In the present study, tomato (Solanum lycopersicum cv. Micro Tom) fruits were used as materials, and different irrigation frequencies were set during the fruit expansion stage. The normal treatment (CK) was irrigated every three days, while the water deficit treatments were irrigated at varying frequencies: once every 4 days (T1), 5 days (T2), 6 days (T3), 7 days (T4), and 8 days (T5). These corresponded to 80%, 70%, 60%, 50%, and 40% of the maximum field moisture capacity (FMC), respectively, with CK maintaining full irrigation at 90% of the maximum FMC. The water deficit treatment T3, with less stress damage to plants and the most significant effect on fruit quality improvement, was selected based on plant growth indices, photosynthetic characteristics, chlorophyll fluorescence parameters, and fruit quality indices, and its effects on carotenoids, glycolic acid fractions, and volatile compounds during tomato fruit ripening were further investigated. The outcome indicated that moderate water deficit significantly increased the carotenoid components of the tomato fruits, and their lycopene, lutein, α-carotene, and β-carotene contents increased by 11.85%, 12.28%, 20.87%, and 63.89%, respectively, compared with the control fruits at the ripening stage. The contents of glucose and fructose increased with the development and ripening of the tomato fruits, and reached their maximum at the ripening stage. Compared to the control treatment, the moderate water deficit treatment significantly increased the glucose and fructose levels during ripening by 86.70% and 19.83%, respectively. Compared to the control conditions, water deficit conditions reduced the sucrose content in the tomato fruits by 27.14%, 18.03%, and 18.42% at the mature green, turning, and ripening stages, respectively. The moderate water deficit treatment significantly increased the contents of tartaric acid, malic acid, shikimic acid, alpha ketoglutaric acid, succinic acid, and ascorbic acid, and decreased the contents of oxalic acid and citric acid compared to the control. The contents of total soluble sugar and total organic acid and the sugar–acid ratio were significantly increased by 48.69%, 3.71%, and 43.09%, respectively, compared with the control at the ripening stage. The moderate water deficit treatment increased the fruit response values to each sensor of the electronic nose, especially W5S, which was increased by 28.40% compared to the control at the ripening stage. In conclusion, during the ripening process of tomato fruit, its nutritional quality and flavor quality contents can be significantly improved under moderate (MD) deficit irrigation treatment. The results of this experiment can lay the foundation for the research on the mechanism of water deficit aiming to promote the quality of tomato fruit, and, at the same time, provide a theoretical basis and reference for tomato water conservation and high-quality cultivation.