The organic material in Chongqing were selected to conduct composting test in order to screen the optimal proportion for fabricating the organic fertilizer products for flue-cured tobacco. The results showed the organic fertilizers could increase the proportion of superior middle, yield and quality of flue cured to bacco compared with the control. The high C/N organic manure (M3, M4 and M5) could significantly increase the proportion and output value of the superior middle of the tobacco leaves. The organic fertilizers (M3, M4 and M5) had the best effect on the nutrient uptake and growth of flue-cured tobacco. The effect of three kinds of high C/N ratio organic fertilizers on the growth of flue-cured tobacco, the quality of tobacco leaves and the coordination of tobacco leaves were better than the current applied cake fertilizer or the mixture of cake fertilizer and farmyard manure, which may be attributed to the comprehensive effects of high C/N ratio on the number of soil microbes and the improvement of soil fertility. In short, in the current tobacco production in Chongqing, the application of organic manure with high C/N ratio, especially the organic manure with the tobacco rod replacing the current cake fertilizer and farmyard manure, is an ideal organic fertilizer in improving tobacco quality effectively.