Irrigation water is essential for greenhouse plants because it is the only water source in the greenhouse. In addition, escalating water costs and expensive fertilizers have raised concerns about adopting advanced technology to improve water and nitrogen utilization efficiency. This study aimed to explore the effects of different water and nitrogen application rates on yield, fruit quality, and water and nitrogen utilization efficiency in southeast China. Plants were irrigated every 7–10 days at different proportions of crop evapotranspiration (ETc) based on the modified Penman–Monteith formula (ET0). The crop coefficient (Kc) was adopted as 0.6, 1.15, 1.15 and 0.9 during the seedling stage, flower stage, the mid-season stage and the end of the season stage, respectively. There were three water levels—0.75 ETc (W1), 1.0 ETc (W2), 1.25 ETc (W3)—and four nitrogen levels—120 (N1), 220 (N2), 320 (N3), and 420 kg N hm−2 (N4)—and a total of 12 treatments, with the application completely randomized by using block design in the experiment. Tomato yield was improved by nitrogen supply. However, nitrogen application had a negative effect on tomato yield when the nitrogen level was applied above 320 N ha−1. The maximum water use efficiency (WUE) value of 30.5 kg m−3 was observed at W2N3, and the maximum nitrogen use efficiency (NUE) value of 684.4 kg kg−1 N was observed at W1 treatment with N1. The net photosynthetic rate of tomato leaves could be increased by reasonably increasing water and nitrogen application. The dry biomass increased with the amount of water and nitrogen in the range of (0.75–1.0) ETc and (120–320) kg ha−1. The best values of tomato quality parameters (Vc, Lycopene, soluble protein et al.) were observed at W2N3. The irrigation level of 1.0 ETc and nitrogen level of 320 N ha−1 was recommended as the best combination of water and nitrogen for greenhouse tomato cultivation in the experimental areas.