Essential macronutrient nitrogen (N) is crucial for plant growth and yield, but excessive chemical N fertilizer not only increases unnecessary production costs but also causes environmental pollution. Therefore, reducing N fertilizer use by increasing organic fertilizer use is crucial for sustainable agriculture. In this study, we investigated the effects of three nitrogen levels—the recommended rate (N), a 20.0% reduced rate (0.8N), and a 40.0% reduced rate (0.6N)—and two levels of organic fertilizer—a normal dose (M) and a four-times the normal dose (4M)—combined with root application of the beneficial element silicon (Si) on the photosynthetic characteristics, yield, and fruit quality of the tomato cultivar ‘Tianxi No. 5’. Compared with M + N treatment, the longitudinal diameter, transverse diameter, fruit weight, and fruit yield of tomato fruit in 4M + 0.6N treatment significantly increased by 12.4%, 14.6%, 14.5%, and 12.8%, respectively, while the yield was further improved with Si application. In addition, a reduction in N fertilizer and an increase in organic fertilizer, combined with Si application, improved fruit quality parameters such as concentrations of vitamin C, lycopene, phenols, flavonoids, sucrose, fructose, etc., and promoted sugar metabolism-related enzyme activity (sucrose synthase, invertase, and sucrose phosphate synthase) and the accumulation of N in the fruit. The principal component analysis and three-factor analysis of variance (ANOVA) of the fruit quality and yield indices showed that nitrogen fertilizer, organic fertilizer, silicon fertilizer, and the interaction of the three had significant effects on the quality and yield of tomato fruits, and that the 4M + 0.6N + Si treatment had the best combined effect on the yield and quality of the tomatoes. Thus, a moderate reduction in chemical N fertilizer, combined with increased organic fertilizer and Si, could be an effective agronomic practice for improving the yield and quality of tomatoes.
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