By studying the response of soil and microbial biomass stoichiometric characteristics to fertilization, it is possible to optimize effective fertilization management during flue-cured tobacco growing periods. In this study, we studied the effect of compound fertilizers combined with microbial fertilizer treatments on stoichiometric characteristics of rhizosphere soil and the limitation of microbial resources during the flue-cured tobacco growth periods. The results indicated that soil and microbial C:N:P varied greatly with the growing period, the effect of sampling time was usually greater than fertilization treatment, and the microbial C: N:P did not vary with the soil resource stoichiometric ratios. With the extension of the growth period, the microbial metabolism of tobacco-growing soil was limited by phosphorus and showed a trend of increasing first and then decreasing. The rhizosphere soil microbial resources nitrogen and phosphorus limitation were mainly affected by soil water content, soil pH, microbial biomass carbon, and the ratio of microbial biomass carbon to microbial biomass phosphorus, and the application of microbial fertilizers can reduce phosphorus limitation. Therefore, the application of microbial fertilizers regulates the limitation of microbial resources by affecting the soil and microbial biomass C: N: P in flue-cured tobacco rhizosphere soils.