Abstract: To investigate the effects of intercropping flue-cured tobacco with different grain and economic crops on soil microecology and tobacco leaf quality, a field experiment was conducted in the tobacco-growing area of Junan County, Linyi City, Shandong Province. With flue-cured tobacco monocropping as the control (CK), three intercropping treatments were established: flue-cured tobacco intercropped with sweet potato (T1), peanut (T2), and soybean (T3). Changes in soil microbial community structure, soil physicochemical properties, enzyme activities, and tobacco leaf quality at different growth stages of flue-cured tobacco were analyzed. The results showed that compared with CK, T3 significantly increased the Shannon index of rhizosphere soil bacteria at the rosette stage, enriched beneficial bacterial genera such as Bacillus, and exhibited the most significant difference in community structure from CK in PCA analysis across all stages. T1 only had a certain impact at the vigorous growth stage and mature stage, while the effect of T2 was relatively weak. In the T3 treatment, soil total nitrogen and available potassium at the rosette stage increased by 37.6% and 7.5% compared with CK, respectively, showing significant improvements; at the vigorous growth stage, total nitrogen increased by 89.8% and organic matter increased by 18.9% compared with CK. The abundance of amo A genes in AOA/AOB increased by up to 45.5%, and soil enzyme activities at the vigorous growth stage and mature stage were enhanced. In the T3 treatment, the contents of auxin and zeatin riboside in tobacco leaves at the vigorous growth stage increased by 38% and 27%, respectively; the contents of nitrogen and magnesium in tobacco leaves increased by 12.4% and 9.6%, respectively, and disease-resistant genes such as PR1 a/c were activated. The appearance quality and sensory quality of upper and middle tobacco leaves under different intercropping patterns were all improved, with the T3 treatment being the best; the T3 treatment significantly increased the total nitrogen and nicotine contents in upper and middle leaves. In conclusion, the flue-cured tobacco-soybean intercropping pattern significantly improves the yield and quality of tobacco leaves by strengthening soil microecology and nutrient cycling, and can be popularized and applied in the study area and similar tobacco-growing regions.