A field experiment was conducted to study the application effects of different organic materials (including conventional commercial organic fertilizer, bio-organic fertilizer and biochar) on soil improvement and flue-cured tobacco yield and quality in order to realize the sustainability of flue-cured tobacco production. The results showed that compared with the local conventional fertilization (100% chemical fertilizer), the combination of organic materials with chemical fertilizers could enhance soil enzyme activities and soil microbial functional diversity, significantly increase potassium content and improve the coordination of chemical composition of flue-cured leaves, promote average price, fine tobacco ratio and economic benefits of flue-cured leaves. Comparatively, the combined application of bio-organic fertilizer and biochar is more effective.