Abstract: Soil microbial flora is an important biological index to measure soil biological fertility and health status. In order to study the effects of the combination of biocontrol agents and organic fertilizer on the microflora of tobacco planting soil. Through field plot experiments, designed test with two factors and complete combination. Determined the number of bacteria, actinomycetes and fungi in tobacco soil of different treatments in different periods. The results showed that: the combination of biocontrol agent and organic fertilizer can roughly increase the number of bacteria and actinomycetes, and reduce the number of fungi, which in tobacco planting soil. In flue-cured flourishing period and maturity period, the number of bacteria in the combination of microbial inoculum and cow manure increased by 101% and 27.6% over cow manure alone. In the combination of microbial inoculum and cow manure or amino acid organic fertilizer, the number of actinomycetes was much more than other tests, especially during the boom period, the number of actinomycetes in the combination of microbial inoculum and amino acid organic fertilizer was higher than other treatments 205.2×104~277.3×104 cfu/g. The combination of microbial inoculum and the shrimp peptide organic fertilizer has the best effect on the soil fungi inhibiting. The number of fungi in flue-cured growth cycle have been at a low level. In summary, the combination of biocontrol agent and cow manure can effectively improve the microflora of tobacco planting soil, change it from "fungal type" to "bacterial type". It is the most suitable combination for Panzhihua to apply in tobacco area.