Abstract: Two pilot-scale deep integrated vertical flow constructed wetland systems (IVCW, total matrix height=180 cm) were constructed with tetrabrominated diphenyl ethers (BDE-47) as target pollutants. Under the conditions of fixed hydraulic retention time (HRT=3d) and hydraulic loading rate (0.3 m/d), the step-by-step removal rate of BDE-47 (influent concentration=25 μg/L) was analyzed, and the effects of polybrominated diphenyl ethers (PBDEs) on the conventional purification efficiency and substrate microorganisms of IVCW systems were discussed. The batch experimental results showed that after three months of operation, the removal rate of BDE-47 in simulated effluent of wastewater treatment plant by IVCW reached 99.9%. Compared with the control group, the removal rate of ammonia nitrogen in BDE-47 treatment group increased from 72.3% to 82.9%, but the removal rate of nitrate nitrogen decreased from 53.0% to 28.1%. Meanwhile, the removal rate of chemical oxygen demand (COD) decreased from 88.1% to 82.3%. The residual amount of BDE-47 in the substrate of each unit of IVCW decreased gradually along the flow direction, and the content of BDE-47 was the highest in the upper unit of downstream flow, which was close to the inflow (0.01 μg/g). A significant decrease in substrate microbial dehydrogenase activity was resulted due to BDE-47 involvement. Correspondingly, microbial fatty acid profile analysis showed that there was a significant difference in microbial community composition of the down-flow units between the experimental and the control groups, which were dominated by more tolerant anaerobic Gram-negative bacteria and fast-growing aerobic Gram-negative bacteria, respectively. The removal potential of BDE-47 and its migration and transformation mechanisms in IVCW could provide useful reference and a feasible scheme for the removal of refractory organic pollutants by ecological engineering systems.