To solve the problem of decreased quality of the tobacco caused by low temperature and overcast-rain at prior period of field growth which inhibit the growth of tobacco in Hunan paddy-tobacco area, flue-cured tobacco variety Yunyan87 was used as the experimental material, and optimized base fertilizer(adding microbial agent) and seedling fertilizer(applying urea), namely, fertilization mode for promoting early growth and rapid development were applied to evaluate the comprehensive effect of the optimized fertilizer on yield and quality of tobacco leaves by analyzing the agronomic characters, dry matter and nitrogen accumulation, economic characters, physical characteristics, chemical composition and sensory smoking quality of the flue-cured tobacco. The results showed that the addition of microbial agent to base fertilizer and special seedling fertilizer combined with urea could increase plant height, maximum leaf length, width and area, increase dry matter and nitrogen accumulation, increase yield and output value of flue-cured tobacco, increase the balanced moisture content and leaf thickness of tobacco leaves, increase the total sugar content of tobacco leaves, reduce the nicotine content, and improve the sensory evaluation and smoking quality of tobacco leaves. The interaction between the two resulted in tobacco leaves with comprehensively higher yield and better quality. The treatment of adding microbial inoculant in basal fertilizer and adding area as seedling-raising fertilizer was better than those of traditional basal fertilizer and seedling-raising fertilizer, the economic character index, smoking quality index and comprehensive effect of index increased 11.27%, 20.01%, and 12.61%, respectively.