Abstract: To explore the effects of different functional carbon-based organic fertilizers combined with microbial agents on tobacco leaf yield and quality, so as to achieve the rational application of functional carbon-based organic fertilizers and microbial agents, a field experiment was conducted. Five treatments were implemented: commercial organic fertilizer (CK), biochar-based fertilizer (T1), hydrothermal carbon-based fertilizer (T2), biochar-based fertilizer + microbial agent (T3), and hydrothermal carbon-based fertilizer + microbial agent (T4). The changes in the growth and development, yield, quality, chemical composition, and sensory evaluation quality of flue-cured tobacco, as well as physical and chemical properties of the tobacco-growing soil under different treatments were analyzed. Compared with conventional organic fertilizer, both carbon-based fertilizers combined with microbial agents (T3, T4) can effectively increase the area of tobacco leaves, and reduce the incidence of climatic spot disease and tobacco mosaic disease. The contents of total sugar and reducing sugar, nitrogen-base ratio and sugar-base ratio are increased while the nicotine content is reduced by T3 and T4 treatments. In addition, the contents of total sugar, reducing sugar, nicotine, total nitrogen and potassium meet the evaluation standards of high-quality tobacco leaves. Compared with CK, both carbon-based fertilizer alone treatments (T1, T2) and carbon-based fertilizer combined with microbial agent treatments (T3, T4) could significantly increase the contents of organic matter by 28.0% - 36.0% and alkali-hydrolyzable nitrogen by 158% - 271% in tobacco-growing soil. The T2, T3 and T4 treatments increase the content of available potassium significantly by 4.36% to 37.7%, while T3 and T4 treatments can effectively reduce soil bulk density. Soil pH is positively correlated with output value, while yield is positively correlated with content of exchangeable magnesium in soil. The application of carbon-based fertilizers combined with microbial agents can improve the soil for tobacco cultivation, increase the content of available nutrients, coordinate the chemical composition and proportion of tobacco leaves, thus facilitating the production of high-quality tobacco leaves, and enhancing the economic benefits of flue-cured tobacco. The application of biochar combined with microbial agents exhibits the best comprehensive effect.