[Background] The large-scale agricultural reclamation and development of oasis ecosystem in Xinjiang have ecological impacts on the environment. Thus, it is important to evaluate the effect of human activities on the soil biological characters, especially the soil bacterial community, to provide a guidance for rational utilization of land and sustainable development of agricultural resources in the future. [Objective] By comparing soil bacterial structure and diversity in cotton fields affected by agricultural reclamation, with those in poplar forests where ecological environment has largely been kept intact, we studied the effects of human activities on agricultural reclamation and development on soil microbial ecology. [Methods] The national standard method was used to measure the soil physical and chemical properties, including total nitrogen, total salt, organic matter, alkaline hydrolysis nitrogen, available phosphorus, available potassium and pH in the cotton fields and poplar forests in the lower and middle reaches of Tarim river basin. Total soil DNA was extracted, a library was established by PCR amplification, and 16S rRNA gene (V4 region) was high-throughput sequenced using Illumina Hiseq 2500 sequencing technology platform. Bioinformatics was used to analyze the changes of bacterial α-diversity (such as Chao1, observed species, phylogenetic diversity (PD), Shannon, Simpson and Good’s coverage indices) and β-diversity in the two areas, and redundancy analysis was used to find the main factors that may have affected the changes of the bacterial community structure in the both areas, as well as community function prediction results were also used to give an auxiliary interpretation. [Results] Basic physical and chemical properties of soil analysis: compared with the primary poplar forest in oasis cotton field, there were significant increases in total nitrogen, alkaline hydrolysis nitrogen, salt and pH, and significant positive correlation between soil salt content and total nitrogen, alkaline hydrolysis nitrogen and pH (P<0.05). Bacterial diversity analysis: the diversity index of chao1, observed species and PD in cotton field samples were significantly lower than those in poplar forest samples. The Shannon index difference was not significant, but it showed the same variation trend with the above three indexes. Bacterial community composition analysis: the dominant bacteria across the two places were Alphaproteobacteria, Actinomycetes, Gemmatimonadetes, Bacteroides, Acidobacteria, Gammaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, Planctomycetes, Crenarchaeota and Nitrospirae (>1%). According to the results of linear discriminant analysis, the significant enriched microorganisms in cotton field soil were Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Flavobacteria and some species of Alphaproteobacteria, Gammaproteobacteria, and one species (Candidatus Nitrososphaera) belonged to Crenarchaeota was also discovered in cotton field. However, in original poplar forest soil samples, the significant enriched microorganisms were Chlorobi, and Deltaproteobacteria. Some species in Proteobacteria and the Nitrosopumilus which belonged to Crenarchaeota was enriched in poplar forest soil. The results of principal coordinates analysis (PCoA) showed that soil bacterial community composition (BCC) of cotton field could be significantly separated from that of poplar forest, and the BCCs in cotton field ecosystem was more consistent. The results of functional prediction showed that nitrification function in cotton field was significantly surpassed the poplar forest. Redundancy analysis showed that the total nitrogen content had a significant effect on the variation of BCC. [Conclusion] Under the influence of long-term cultivation, fertilization and other human activities, the soil bacterial diversity and community composition of oasis cotton field have been significantly changed, the α-diversity of bacterial community was significantly lower than that of the poplar forest, the β-diversity of bacterial community was weakened, and some bacteria related to plant growth, such as Actinobacteria and nitrifying bacteria, have been significantly enriched. This result can provide useful information to utilize and develop Xinjiang oasis ecosystem filed in near future.