Background: Manganese (Mn) stress is an important reason for forming tobacco ( Nicotiana tobacum L. ) leaf browning, leading to low yield and quality of tobacco leaves. The mechanism of flue-cured tobacco varieties, Honghuadajinyuan (Hongda) and K326 tobacco leaves browning by Mn were explored. The two tobacco varieties were planted in red soil and sandy soil and Mn concentration of 0, 250, 500, 750 and 1000 mg/kg were applied. The research investigate the traits of agronomic, physiological and economic of flue-cured tobacco. Results: As Mn application rate increased, browning scale increased while plant height, root, stem and total weight, content of chlorophyll decreased. Activities of superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) showed a rising parabolic formation. As Mn application rate increased, the content of malondialdehyde (MDA) and relative conductivity increased. Peroxidase (POD) activity continually increased with Mn application rate in K326 variety, while in Hongda variety, POD activity first increased and then decreased in sandy soil, while it continuously rose in red soil. Mn concentration and browning scale were significantly and negatively correlated with height, soil and plant analysis development (SPAD), CAT, total weight, average priceand yield, but significantly positively correlated with total plant Mn content, POD and MDA. Plant Mn concentration was significantly and positively correlated with browning scale. This study founded that SOD, CAT, APX, POD enzyme activity and MDA content in tobacco leaves affected by Mn concentration in soils, cause the change of chlorophyll content, agronomic and economic traits of flue-cured tobaccos. Conclusion: The mechanism of Mn stress to the physio-biochemical of tobacco varieties would be useful for controlling browning tobacco leaves by agronomic strategies and regarding as markers for Mn tolerance in breeding.