To explore the effects of continuous planting of flue-cured tobacco on soil physiochemical properties and microbial community diversity, and to identify the main factors leading to continuous cropping obstacles, rhizosphere soils of continuous cropping (CCO) and non-continuous cropping tobacco fields (NOR) in Lijiang of Yunnan Province were collected. Soil nutrients, enzyme activities and microbial diversity were measured, and the differences in bacterial and fungal community diversities and network structures between CCO and NOR soils were analyzed. The relationship between soil physiochemical properties, microbial communities and tobacco plant growth was analyzed by partial least squares (PLS) model. The results showed that the plant height and fresh weight of CCO was significantly reduced by 50.27% and 71.09% compared with NOR. The available phosphorus, potassium and conductivity of CCO soil increased by 129.66%, 40.90% and 132.74%, respectively, and soil urease activity increased significantly, but soil pH decreased by 0.45 units, and acid phosphatase activity decreased significantly. The bacterial community showed a significant decrease in Shannon and phylogenetic diversity (PD) indexes, whereas fungal community displayed significant increases in ACE, Shannon, and PD indexes. Bacteria and fungi such as Rhodococcus, Streptomyces, Cellvibrio, Cyphellophora, Gibberella, Ceratocystidaceae, and Waitea were enriched. Co-occurrence network analysis indicated that CCO soil microbial network had higher modularity and tighter connection, and the competition between bacteria was enhanced, while the competition between fungi was weakened. PLS analysis showed that soil available phosphorus had a significant positive effect on microbial community, while soil conductivity had a significant negative effect. The change of microbial community was the main reason for the obstacle of continuous cropping in tobacco field.