With the same inorganic fertilizer rates, effects of applying fully-fermented organic manure on flue-cured tobacco root development and leaf quality were studied. The results indicated that organic manure could enhance the development of the flue-cured tobacco's first and second order lateral roots. The volume and dry mass of the first and second order lateral root increased with the increase of growth period and the increasing range in organic manure treatments was bigger than that of control. Compared with the control, applying organic manure could improve the length, amount, volume and dry mass of the first and second order lateral root and root vigor. It could also reduce the contents of total sugar and reducing sugar, yet increase the contents of total nitrogen, nicotine and protein in B2F. It could increase the contents of total sugar and reducing sugar in C2F and nicotine and potassium in X2F. The scores of aroma volume, after taste, offensive odor, lingering odor scores and the total score of sensory quality of C2F were higher than that of control.