In order to clarify the application effect of root-promoting and nitrogen-reducing fertilization mode in southern rice-growing tobacco areas, the effects of root-promoting and nitrogen-reducing fertilization mode (reducing the proportion of nitrogen in base fertilizer，applying base fertilizer in root zone, adding root setting water-fertilizer and water-soluble top-dressing, changing the special base fertilizer and top-dressing formula and the amount of application) on appearance quality, physical characteristics, chemical composition, smoking quality, economic traits and economic effect of flue-cured tobacco were studied with traditional fertilization mode as the control. The results showed that root-promoting and nitrogen-reducing fertilization mode was benefit to improve the appearance quality of tobacco leaves, improve the single leaf weight and leaf specific weight of upper tobacco leaves, reduce nicotine content, improve the smoking quality of upper and middle tobacco leaves, improve the first-class tobacco proportion, average price and output value of upper tobacco leaves. Moreover, it save 5.81% of labor, save 3.27% of agricultural materials cost, increase 23.37% of net income, the input-output ratio increased by 6.29%, the nitrogen partial factor productivity increased by 28.11%, and the nitrogen partial production benefit increased by 33.79%. Under the condition of nitrogen reduction of 22.22%, the root-promoting and nitrogen-reducing fertilization mode improves the economic and environmental benefits of paddy-tobacco, and has promotion value in southern rice-growing tobacco areas.