[Background] River confluences have become a focus in ecological management of a river basin. [Objective] The microbial community structure and main influencing environmental factors at the estuary of the Fenhe River into the Yellow River were studied. [Methods] The microbial community structure at estuary of the Fenhe River into the Yellow River in summer was analyzed by means of 16S rRNA gene-based Illumina Miseq high-throughput sequencing, and the main environmental factors affecting the microbial community were identified by canonical correspondence analysis. [Results] The alpha-diversity analysis revealed that the diversity of microbial community was high in this area. Microbial diversity analysis indicated that the dominant bacterial phyla were Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria; at genus level of taxonomic criteria, the dominant genus was Bacillus, followed by Lactococcus and hgcI_clade. Spearman correlation analysis and canonical correspondence analysis (CCA) showed that environmental factors had significant effects on the microbial community structure of water. [Conclusion] The microbial community composition was different between the Fenhe River and the Yellow River, different environmental factors had distinct effects on diverse microorganisms. The microbial communities were mostly affected by pH and dissolved oxygen (DO) at the estuary of the Fenhe River into the Yellow River.