Abstract: In order to further study the effect of tobacco black shank disease on tobacco quality, compared the different physiological indexes of flue-cured tobacco varieties, black shank disease incidence and the relationship between the relevant chemical composition, with flue-cured tobacco ‘Hongda’, ‘K326’and ‘Yunyan85’ varieties as material under the same condition. Result: the black shank disease incidence and disease index of ‘Hongda’ is the highest, ‘K326’ take the second place, and ‘Yunyan85’ is the lowest. The activity of POD, PPO, CAT, total phenol and flavonoids of ‘Yunyan85’ is highest and the increase is the largest in vaccination, ‘K326’ second, ‘Hongda’ minimum. The activity of PPO, CAT, POD are negative corrected with flavonoids and total phenol, and positive correlated with protein and soluble sugar.