[Background] Tobacco is one of the most important economic crops in China, and its characteristics of avoiding continuous cropping have seriously affected the development of tobacco industry in China. [Objective] The relationship between tobacco continuous cropping obstacles, soil physical and chemical properties and microbial diversity was studied to provide a theoretical basis for solving tobacco continuous cropping obstacles and formulating effective tobacco production techniques. [Methods] Tobacco fields with serious continuous cropping obstacles and tobacco fields that overcome continuous cropping obstacles were selected as research objects. Based on high-throughput sequencing technology, the relationship between continuous cropping obstacles, physical and chemical properties of tobacco fields and soil microbial diversity was studied. [Results] The contents of pH, total nitrogen and organic matter in tobacco fields overcoming continuous cropping obstacles were significantly higher than those in tobacco fields with serious continuous cropping obstacles. There was no significant difference in soil microbial diversity between tobacco fields overcoming continuous cropping obstacles and serious continuous cropping obstacles, but soil microbial dominant communities changed significantly. pH, organic matter, available phosphorus and total nitrogen in tobacco soil were significantly correlated with microbial community. [Conclusion] The difference of overcoming the obstacle of continuous cropping in tobacco field may be related to the difference of soil physical and chemical properties and microbial composition in tobacco field. This study provides theoretical basis and technical support for solving the problem of continuous cropping obstacles in Xiangxi tobacco area.