Against the background of global climate change and China’s “dual carbon” strategy, assessing and enhancing the carbon sequestration and emission reduction capacity of farmland ecosystems is of great importance. As an important economic crop in China, flue-cured tobacco still lacks systematic studies on ecosystem carbon budgets involving novel carbon-enrichment materials and fine-scale accounting at the township level. In this study, Zhongcun Township, Lufeng City, Chuxiong Prefecture, Yunnan Province, was selected as a representative area. Based on farmer questionnaire surveys and a field positioning experiment, a field-stage carbon accounting model for the flue-cured tobacco ecosystem was established. Four treatments were set up: conventional tobacco-specific fertilizer only as the control (CK), tobacco-specific fertilizer combined with calcium silicate and bio-organic fertilizer (T1), tobacco-specific fertilizer combined with calcium silicate and biochar (T2), and tobacco-specific fertilizer combined with calcium silicate, biochar, and bio-organic fertilizer (T3). The effects of mesoporous calcium silicate, biochar, and bio-organic fertilizer application on the system carbon budget were quantitatively evaluated. The results showed that the flue-cured tobacco ecosystem under CK acted as a net carbon source, with a net carbon balance of -0.75 tCO2·hm-2·yr-1. After the application of carbon-enrichment materials, the system carbon budget responses differed markedly among treatments. Although T1 increased post-harvest residue carbon input and soil carbon sequestration, it still acted as a net carbon source, with a net carbon balance of -0.87 tCO2·hm-2·yr-1. In contrast, T2 and T3 formed net carbon sinks of 0.38 and 1.21 tCO2·hm-2·yr-1, respectively. T3 showed the highest soil carbon sequestration, reaching 9.14 tCO2·hm-2·yr-1, and increased the net carbon balance by 1.96 tCO2·hm-2·yr-1 compared with CK. Its carbon ecological efficiency reached 1.14, indicating a relatively high carbon sink return per unit carbon emission. Overall, biochar-containing carbon-enrichment treatments improved the field-stage net carbon balance of the flue-cured tobacco ecosystem. Among them, the combined application of calcium silicate, biochar, and bio-organic fertilizer showed a better overall effect, providing a reference for carbon sequestration and emission reduction management in tobacco fields.