Microorganisms play a key role in removal of pollutants in constructed wetlands ( CWs). The aim of this study was to investigate the composition and diversity of microbes in a full-scale integrated constructed wetland system and examine how microbial assemblages were shaped by the structures and physicochemical properties of the sediments. The microbial assemblages were determined using 16S rRNA high-throughput sequencing. Results showed that the microbial phenotypes were more diverse in the system than in single CWs. The genera of Zoogloea, Comamonas, Thiobacillus, Nitrosospira, Denitratisoma, Azonexus, and Azospira showed relatively high abundances, which contributed to the removal of organic matter and nitrogen. The interactions among the three CWs in series acted a key role in the increase of phylogenetic diversity and high percentage of shared operational taxonomic units. In the system, some core microbes always existed even with the changing environment. Redox potential and NH4-N were the important factors affecting the overall microbial community patterns. Total organic carbon had a relatively high impact on some denitrifiers. The results from this study should be useful to better understand the microbial mechanism of wastewater treatment in integrated constructed wetland systems.