Tomatoes have high nutritional value and abundant bioactive compounds. Moderate water deficit irrigation alters metabolic levels of fruits, improving composition and quality. We investigated the effects of water deficit (T1, T2, T3, and T4) treatments and adequate irrigation (CK) on tomato polyphenol composition, antioxidant capacity, and nutritional quality. Compared with CK, the total flavonoid content increased by 33.66% and 44.73% in T1 and T2, and total phenols increased by 57.64%, 72.22%, and 55.78% in T1, T2, and T3, respectively. The T2 treatment significantly enhanced antioxidant’ capacities (ABTS, HSRA, FRAP, and DPPH). There were multiple groups of significant or extremely significant positive correlations between polyphenol components and antioxidant activity. For polyphenols and antioxidant capacity, the classification models divided the treatments: CK and T4 and T1–T3. The contents of soluble solids, soluble protein, vitamin C, and soluble sugar of the treatment groups were higher than those of CK. The soluble sugar positively correlated with sugar–acid ratios. In the PCA-based model, T3 in the first quadrant indicated the best treatment in terms of nutritional quality. Overall, comprehensive rankings using principal component analysis (PCA) revealed T2 > T1 > T3 > T4 > CK. Therefore, the T2 treatment is a suitable for improving quality and antioxidant capacity. This study provides novel insights into improving water-use efficiency and quality in the context of water scarcity worldwide.