Purpose <p>This study aimed to explore the effects of different fertilization practices on soil respiration and carbon balance in vegetable fields within the subtropical red soils of southwest China.</p> Methods <p>The trial utilized a long-term fixed plot design conducted over 16 years (2007–2023). Five fertilization treatments were established: no fertilizer application (CK), organic fertilizer (OM), chemical fertilizer and organic fertilizer (NPK + OM), additional nitrogen fertilizer (NPK + OM + N), and additional phosphorus fertilizer (NPK + OM + P).</p> Results <p>In comparison to the OM treatment, the cumulative total soil respiration emissions under the combined application of organic and inorganic fertilizers were significantly reduced by 77.2–79.5% during the lettuce growing season and by 23.8–49.5% during the cabbage growing season. Furthermore the cumulative emissions of heterotrophic respiration in the soil was significantly reduced by 75.4–77.2% in the lettuce growing period and by 34.6–38.2% in the cabbage growing period as a result of the combined application of organic and inorganic fertilizers. No significant differences were observed among the NPK + OM, NPK + OM + N, and NPK + OM + P treatments. During the lettuce growing period, the land acted as a carbon source, primarily due to carbon release from soil microbial heterotrophic respiration, while during the cabbage growing period, it functioned as a carbon sink, primarily due to carbon fixation in crop biomass.</p> Conclusions <p>In managing upland vegetable fields within the subtropical red soils of southwest China, it is essential to prioritize the integrated use of organic and inorganic fertilizers. This approach not only mitigates carbon emissions but also contributes to the maintenance of carbon balance.</p>