In order to determine the effects of different microbial fertilizers on the growth，the accumulation and distribution of dry matter and nutrient of flue-cured tobacco，and provide technical supports for promoting early growth and rapid development of flue-cured tobacco intercropped with rice，‘Yunyan 87’ was used as material in Guiyang County，Chenzhou City，Hunan Province.The effects of application of microbial fertilizers in root zone such as Dunfeng nano-silica fertilizer，Ploughing the World microalgae nutrient solution，Golden-leaf microbial fertilizer and Rhizome Kang microbial fertilizer on flue-cured tobacco growth，dry matter and nitrogen，phosphorus and potassium accumulation，dry matter accumulation efficiency of nitrogen，phosphorus and potassium fertilizer and absorption efficiency of nitrogen，phosphorus and potassium fertilizer were studied.The results showed that:(1)The application of microbial fertilizer in root zone promoted the growth of flue-cured tobacco，and increased the total root length，root surface volume，root volume，root tip，plant height，stem circumference and maximum foliar volume by 1.52%-19.13%，13.32%-45.05%，18.38%-62.23%，8.77%-38.54%，0.74%-3.54%，3.45%-10.69% and 7.10%-16.95%，respectively.The effects of the application of "ploughing the world" microalgae nutrient solution and Golden-leaf microbial fertilizer on promoting the growth of flue-cured tobacco were relatively better.(2)The application of microbial fertilizer in root zone promoted the accumulation of dry matter and nitrogen，phosphorus and potassium.The accumulation of dry matter，nitrogen，phosphorus，and potassium at cluster stage was increased by 7.25%-64.07%，95.36%-380.44%，22.99%-75.16%，and 1.25%-60.24%，respectively，at the peak stage they were increased by 13.05%-23.20%，50.08%-104.89%，6.76%-51.69%，and 0.99%-25.44%，respectively，at the dome stage they were increased by 1.55%-20.30%，9.75%-48.81%，5.68%-13.25%，and 7.53%-18.15%，respectively.Among them，the application of Golden-leaf microbial fertilizer had the best effect on improving the dry matter accumulation and phosphorus and potassium accumulation of flue-cured tobacco，and the application of Dunfeng nano-silicon fertilizer had the best effect on nitrogen accumulation.(3)The application of microbial fertilizer in root zone improved the dry matter accumulation efficiency of nitrogen，phosphorus and potassium fertilizer by 1.55%-20.30%，tobacco production efficiency by 3.14%-27.40%，fertilizer absorption efficiency by 9.76%-48.81%.Among them，the effect of application of Golden-leaf microbial fertilizer on improving fertilizer dry matter accumulation efficiency，tobacco leaf production efficiency and phosphorus fertilizer，potassium fertilizer absorption efficiency was the highest，and the effect of application of Dunfeng nano-silicon fertilizer on improving nitrogen fertilizer absorption efficiency was the highest.(4)Application of microbial fertilizer in root zone improved sugar content and identity of tobacco leaf，appearance quality and smoking quality of tobacco leaf，and increased yield and output value of tobacco leaf.To sum up，in the intercropping area of tobacco with rice，the application of microbial fertilizer in the root zone of flue-cured tobacco could promote the growth of flue-cured tobacco，increase the accumulation of dry matter and nutrients，and improve the fertilizer use efficiency，and improve the yield and quality of tobacco leaves，among which the effect of Golden-leaf microbial fertilizer was the best.