The fungus and bacteria was continuously separated and counted from lower, middle and upper leaves of flue-cured tobacco to analyze the amount and changes of prevalent microorganism during curing process of flue-cured tobacco leaves. Results showed that the amount of fungus on leaves at different stalk positions increased after declining for the first change, and came to the maximal point at the dry-bulb temperature of 42 ℃ when the leaves became totally yellow. The amount of bacteria gradually increased from flue-curing stage, and came to the highest maximal point at the dry-bulb temperature of 38 ℃. Dominant microorganism on tobacco leaves from different stalk positions was different during curing process. Five prevalent fungus was identified, and the highest frequency of occurrence occurred in Penicillium and Aspergillus. Eleven prevalent bacterium was identified, in which the highest frequency of occurrence was Corynebacterium, Enterobacter, Arthrobacter and Pantoea.