<p>The DeNitrification-DeComposition (DNDC) model has been widely used to simulate soil carbon and nitrogen cycling in open-field agroecosystems. However, its performance under greenhouse cultivation remains insufficiently evaluated. This study assessed the ability of the DNDC model to reproduce soil carbon and nitrogen dynamics in a greenhouse tomato system. Field observations and model simulations were further combined to examine the effects of elevated CO₂ (eCO₂) enrichment on soil carbon emission, soil nitrogen dynamics, tomato physiological responses, and yield under different fertilization regimes. Results showed that the DNDC model showed good performance in simulating temporal changes in soil organic carbon, ammonium nitrogen, and nitrate nitrogen under eCO₂ fertilization, with model efficiency values exceeding 0.66. Under eCO₂ combined with chemical fertilizer application, total soil carbon emission decreased to 3120.34&#xa0;kg·ha⁻¹, which was approximately 1.9 times lower than that in CK. Elevated CO₂ also improved tomato physiological performance under the greenhouse conditions of this study, as reflected by increases in net photosynthetic rate, intercellular CO₂ concentration, stomatal conductance, and transpiration rate. These responses were associated with enhanced plant carbon accumulation and ultimately contributed to increased tomato yield. These findings highlight the potential of DNDC for greenhouse carbon–nitrogen assessment and of eCO₂-based fertilization management for improving tomato productivity.</p>