In this study, the influence of deficit irrigation (two watering levels: W1, full and W2, 2/3 deficit) at early or later fruit maturation stages, and reduced nitrogen application (two levels: N1, control and N2, 2/3 reduced) from spring to summer in 2012 (the spring-summer season, SS) and from winter in 2012 to spring in 2013 (the winter-spring season, WS) on greenhouse-grown tomato (Lycopersicon esculentum Mill.) was identified. The treatments were set as: CK (W1W1N1), T1 (W2W1N1), T2 (W1W2N1), T3 (W2W2N1), T4 (W2W1N2), T5 (W1W2N2), T6 (W2W2N2) and T7 (W1W1N2). The results indicated that the fruit yields under deficit irrigation were reduced by 8.6–12.5% and 13.1–29.4% in the two seasons, respectively. The contents of TTS (total soluble solids), TSSC (total soluble sugar content), SAR (sugar and organic acid content ratio), VC (vitamin C), lycopene, and RS (reducing sugar) in the fruits of all the plants increased during the maturation in the WS season. Crop evapotranspiration (ETc), contents of TTS, TSSC, SAR and VC were all increased in the treated fruits compared to the control ones (CK) in both seasons. According to the two-way ANOVA, the fruit quality was more sensitive to water than to N-fertilizer, but it was just the opposite for NC (nitrate content). GRA (gray relational analysis method) and PCA (principal component analysis method) were two suitable appraisement methods for fruit comprehensive quality analysis. Eventually, the combinational evaluation method showed that T3 (W2W2N1) was the best water and nitrogen management strategy for the fruit comprehensive quality and yields in tomato.