Water and nitrogen are two main factors affecting crop yield and quality, and their optimization is crucial for sustainable agriculture production. In this study, the results of a three-year (2017–2019) experiment were presented to reveal the effects of irrigation and nitrogen rate on yield, crop water productivity (WP), nitrogen use efficiency (Partial Factor Productivity Nitrogen, PFPn) and fruit quality. Irrigation was applied based on the cumulative evaporation (Epan) measured with a standard 20-cm pan with its amounts set as 50% (I1), 70% (I2), 90% (I3) of Epan, while the nitrogen rates were designed as 0 (N0), 150 (N1), 300 (N2) and 450 (N3) kg ha−1. Averaging across nitrogen rates and years, I2 decreased tomato yield and PFPn by 4.00% and 4.07%, respectively, when compared with I3, while significantly increased WP, vitamin C (Vc), total soluble solid (TSS), soluble sugar content (SSC) and organic acids (OA) by 7.68%, 8.64%, 5.42%, 7.15% and 7.15%, respectively. Averaging across irrigation amounts and years, applying nitrogen rates more than 300 kg ha−1 not only failed to increase yield, but also reduced WP, Vc, SSC, sugar-acid ratio (SAR) and PFPn. Compared with N2, the yield, WP and fruit quality decreased slightly in N1, whereas the nitrogen rate decreased by 50%. Both the principal component analysis and gray relational analysis were identified as suitable models for assessing comprehensive fruit quality. The relative value of TSS had a highly positive relationship with comprehensive quality score, indicating that TSS could be used as an index representing comprehensive fruit quality. TOPSIS (technique for order preference by similarity to ideal solution) revealed that N1I2 was the optimal irrigation and nitrogen rate for greenhouse grown tomato.
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