This paper focused on revealing the mutative regularity of rhizospere micorobe and enzyme activity of flue-cured tobacco, expounding the concerted effect mechanism among flue-cured tobacco, soil and microbe, and disclosing the ecological effects of photosphere microbes in different soil types of flue-cured tobacco. The results showed that there were significant differences in soil rhizosphere microbial flora and cultivated microbial physiological flora between different soil types and different growing periods of flue-cured tobacco, bacteria and potassium bacteria were more suitable in the clayed soil and the sand soil of dark brown forest soil, and the great changes of fungi amount in Albic Planosol might be the reason of poor flue-cured tobacco quality. The changes of actiomycetes in the clayed soil and the sand soil of dark brown forest soil were greater than in Albic Planosol. The most appropriate growing period of ammonifying bacteria was in the following order of clayed soil of dark brown forest soil, sand soil of dark brown forest soil and Albic Planosol. Phosphorus bacteria amount in the clayed soil of dark brown forest soil was significantly higher than in the other two soil types, and abiogenous azotobacter amounts in the clayed soil and the sand soil of dark brown forest soil were significantly higher than in Albic Planosol in the 100st day after transplanting. Furthermore, the results showed that the change of hydrogen peroxidase activity was greatly affected by soil types, and the changes of invertase and polyphenol oxidase activity were less affected by soil types, but their amounts were influenced by soil types.