Abstract: To investigate the effects of applying enzyme liquid fertilizer made from fruit and vegetable waste on the output value of flue-cured tobacco and the microorganisms in the rhizosphere soil for tobacco planting, the Yunyan 87 variety of flue-cured tobacco was used as the experimental material. Field experiments were conducted with three treatments: no enzyme liquid fertilizer (CK); enzyme liquid fertilizer made from cabbage waste (FC); and enzyme liquid fertilizer made from navel orange waste (FO). The effects of these treatments on the growth, yield and output value of flue-cured tobacco were studied, as were the differences in the microbial community structure and diversity of the rhizosphere soil for planting flue-cured tobacco. The main environmental factors affecting rhizosphere soil microorganisms were also revealed. The results showed that compared with the control treatment (CK), the plant height, stalk circumference, effective leaf number, maximum leaf length and maximum leaf width of the flue-cured tobacco increased by 16.33%, 14.53%, 11.11%, 10.43% and 10.31% respectively in the FO treatment, and the output value and proportion of high-grade leaves increased by 15.16% and 20.84% respectively. The organic matter content of the rhizosphere soil increased significantly, by 13.54% compared to CK. The relative abundance of Proteobacteria and Bacteroidota in the rhizosphere soil (21.67% and 3.43%, respectively) was significantly higher than those in the CK sample. The relative abundance of Basidiomycota in the rhizosphere soil was highest at 24.44%. Soil available phosphorus (AP) was a key environmental factor driving changes in bacterial community structure. Enzyme liquid fertilizer made from navel orange waste optimizes bacterial and fungal community structure and diversity in rhizosphere soil, thereby improving the soil biochemical environment and increasing the growth and output value of flue-cured tobacco.