Abstract: Organic agriculture is a sustainable alternative to conventional agriculture. However, little is known about the effect of both organic and conventional agriculture on the environment and on the soil microbial community. The hypothesis was that bacterial community structure is defined by different agronomic practices. The objective of this study was to show how cropping systems, organic and conventional facility management regimes affect bacterial community structure and diversity. The study was also intended to increase knowledge on the prediction of soil sustainability under specific agronomic practices. The Illumina platform Hiseq 2500 high-throughput sequencing technique was used to sequence facility soil bacteria 16S rRNA from 6 treatments (OS:organic management of Solanaceous vegetable continuous cropping; OL:organic management of leafy vegetable continuous cropping; OSL:organic management of leafy-Solanaceous vegetables rotation; CS:conventional management of Solanaceous vegetable continuous cropping; CL:conventional management of leafy vegetable continuous cropping; and CSL:conventional management leafy-Solanaceous vegetables rotation) in Shunyi District of Beijing in June 2016. A total of 17 278 operational taxonomic units (OTUs) and 318 851 effective sequences were detected in the sequence control condition. Compared with soil bacterial community composition, diversity, relative abundance and interaction between soil factors and bacteria in different treatments, the results showed great differences between organic and conventional soil samples in bacterial community composition, and with a higher diversity in organic management. Obvious differences were observed between crop rotation and continuous cropping for bacterial community composition under organic management, while there was no significant difference between crop rotation and continuous cropping for bacterial community composition under conventional management. Soil bacterial diversity for rotation treatments was higher under organic management. It was found that there were mainly 14 genera of bacterial community, including Sphingomonas (5.05%) and Bacillus (4.84%). The abundance of the 14 genera changed significantly between organic and conventional management. There were insecticides degrading bacteria (Sphingomonas, Pseudomonas and Agromyces), disease controlling bacteria (Blastococcus and Lysobacter) and nitrification promoting bacteria (Candidatus Entotheonella and Microvirga) in conventional system. There were plant growth promoting bacteria (Bacillus) and organism degrading bacteria (Arthrobacter, Bhargavaea, Bryobacter, Candidatus Solibacter, Acidothermus and Tumebacillus) in organic system. Redundancy analysis also showed that soil bacterial community was affected mainly by soil total phosphorus, available phosphorus, and soil organic matter. Organic matter-decomposing bacteria Tumebacillus, Candidatus Solibacter and Acidothermus were positive associated with soil organic matter content. Therefore, the difference between organic and conventional soil samples for bacterial community originated from different fertilizer use methods, insecticide use methods and management patterns. Crop rotation promoted soil nutrient cycle and disease control under organic management. The results suggested that ecological adaptation mechanisms of different functional micro-organisms had significant differences in facility vegetable soils under different facility management regimes. The study provided the basis for further studies on exploring and explaining the characteristics and adaptation mechanisms of micro-organisms in facility soils under different facility management regimes.