The soil physical and chemical properties, microbial content and enzyme activity of tobacco-planting soil in 0, 3, 6, 9 years of continuous cropping were determined in Malong of Qujing, Changes in soil nutrient content, microbial content and enzyme activity across different continuous cropping years were analyzed. The results showed that as the number of consecutive years of tobacco cropping increased, soil pH, organic matter, available boron, available copper, available zinc, and available manganese all tended to decrease. In contrast, soil nitrogen, phosphorus, potassium, available sulfur, exchangeable calcium, and exchangeable magnesium showed increasing trends, while chloride ion content first increased and then decreased. Bacterial counts initially declined and then increased with longer continuous cropping, whereas fungal and actinomycete counts continuously increased, and the population of the black stem rust pathogen rose year by year. Urease and sucrase activities exhibited a significant decline, whereas acid phosphatase and peroxidase activities did not show significant differences among years. In conclusion, long-term continuous cropping has led to the imbalance of key nutrients and the deterioration of microbial flora. Therefore, it is suggested that Malong tobacco area should focus on the following points in continuous cropping management: improving acidified soil and supplement organic matter; controlling the excessive application of nitrogen, phosphorus, potassium and sulfur, and supplement trace elements such as boron, copper, zinc and manganese; regulating soil microbial flora to reduce the risk of soil-borne diseases. This study provides a theoretical basis and practical guidance for alleviating continuous cropping obstacles and improving soil health in Malong tobacco area.