Bio-organic fertilizer was utilized widely in agricultural production, in order to explore the work effect of bio-organic fertilizer application on flue-cured tobacco production; this article researched on the effect of the application of bioorganic fertilizer to the growth and development, yield and quality of FCV through field experiments. The results showed that the application of bio-organic fertilizer had no positive effect on the growth of tobacco plants, but it improved significantly the yield, output value, proportion of high-middle class leaves and average price. Compared to control, the yield increased 319.5~600.0 kg/hm2, the output value increased 7090~7890 yuan/hm2, the proportion of high-middle class leaves increased 4.1%~5.7%, the average price increased 1.0~1.3 yuan/kg. The application of bio-organic fertilizer improved the quality of aroma and residual taste, respectively, reduced offensive odor, smoking quality was improved significantly.