To study the impact of different water‐nitrogen regulation modes on the carbon cycle of greenhouse tomatoes and determine optimal irrigation and nitrogen application levels to enhance carbon absorption and minimize greenhouse gas emissions. This study employed three irrigation levels (100%, 80%, and 60% of ET0) and three nitrogen application levels (240, 192, and 144 kg·ha−1), along with a control group (W1N1, i.e., 100% ET0‐240 kg·ha−1). Gas‐chromatography methods were used to monitor CH4 and soil CO2 emissions, while assessing dry matter, carbon content, and carbon fixation capacity of tomato organs throughout the growth period. Additionally, a system for evaluating the net ecosystem carbon budget of facility tomatoes was developed based on net primary productivity. Results indicated reduced CH4 and soil CO2 emissions with decreased irrigation and nitrogen application. Dry matter, carbon content, and carbon fixation of tomato organs initially increased with reduced nitrogen and irrigation but then declined. The W2N2 (80% ET0‐192 kg·ha−1) treatment showed maximal values for dry matter, carbon content, carbon fixation, net primary productivity (NPP), and gross primary productivity (GPP). Findings suggest a positive net ecosystem carbon budget under reduced water and nitrogen conditions, indicating carbon absorption. Specifically, the W2N2 treatment outperformed others in net carbon absorption, highlighting its potential as an effective mode for enhancing carbon sequestration in the region.