In order to understand the mechanism why rapeseed cake application could improve the quality of flue-cured tobacco, a field experiment was conducted to investigate the effect of different fertilization, especially rapeseed cake on the microorganism in rhizosphere soil of flue-cured tobacco. The results showed that fertilization with rapeseed cake increased most significantly the amounts of microbes. However, too many ammonifying and nitrifying bacteria could impede the yellowing and maturity of tobacco leaves during maturity stage. It is important to apply cake fertilizer at proper time and in suitable rate to tobacco .