To investigate the quantitative response of tomato yield and fruit quality to deficit irrigation applied at different growth stages, greenhouse experiments were conducted in 2017 and 2018. Three irrigation treatments (full irrigation and two-thirds or one-third of full irrigation) were applied to greenhouse-grown tomato plants at flowering and fruit development (stage 2) and at fruit maturation stage (stage 3). Grey relational analysis (GRA), the technique for order preference by similarity to an ideal solution (TOPSIS), and principal components analysis (PCA) were used to calculate the comprehensive fruit quality indexes, and combinatorial evaluation method was determined. The results showed that deficit irrigation significantly reduced evapotranspiration (ET) and tomato yield and that relative yield had a negative linear correlation with relative seasonal water deficit (1−ETi/ETc). However, deficit irrigation improved fruit quality, especially at stage 2. Total soluble solids, the total soluble sugar concentration, the sugar-to-acid ratio, and vitamin C in the tomatoes all increased significantly in plants that were deficit irrigated compared with fully irrigated plants, while organic acids and lycopene decreased in both years. There were linear correlations between fruit quality parameters and 1−ETi/ETc. The comprehensive quality index derived from GRA and PCA is reliable, and the comprehensive quality indexes given by GRA, PCA, and a combination of GRA and PCA showed positive linear correlation with 1−ETi/ETc. The comprehensive quality ranking showed that in both years, F2/3M1 (two-thirds full irrigation at stage 2) gave a better result and CK (full irrigation) the worst. An appropriate water deficit at the flowering and fruit development stage, which results in a trade-off between acceptable yield and improved fruit quality, is recommended. Our results provide a sound basis for tomato production that has a desirable balance between high yield and high fruit quality.