Using flue-cured tobacco variety “Longjiang 911” as test material, this paper studied the variations of soil enzyme activities and microbial flora in different arable layers (0-10 cm and 10-20 cm) under continuous cropping of flue-cured tobacco for 1 and 5 in field experimental conditions. The results showed that activities of acidic phosphatase and urease in soil for 1a-continuous cropping was enhanced compared to rotational cropping (soybean-wheat- tobacco), but decreased significantly for 5a-continuous cropping. Soil catalase activity of 5a-continuous cropping decreased by 35.47% compared with 1a-continuous cropping in 0-10 cm layer. The soil sucrase activities of flue-cured tobacco continuous cropping for 1a and 5a showed a greater decrease trend in 0-20 cm layer, which decreased by 30.27% and 52.14% respectively compared to the rotational cropping. Continuous cropping of flue-cured tobacco decreased the numbers of soil bacteria and actinomyces while increased the numbers of soil fungi. The amounts of ammonifying bacteria, aerobic azotobacter and anaerobic cellulose-decomposer decreased for 5a-continuous cropping compared to 1a continuous cropping. Thus, the balance destruction of soil microbial communities and decreases of soil enzyme activity could be attributed to one of the reasons for the continuous cropping obstacle in flue-cured tobacco production.