Eutrophication often leads to the periodic proliferation of harmful cyanobacterial blooms (HCBs), which threaten the sustainability of freshwater ecosystems and lead to serious environmental, health and economic damage. Hence, it is vitally important to take effective measures to manage HCBs and associated problems. In this study, vertical flow constructed wetlands (CWs) were operated under different hydraulic loading rates (HLRs) to treat a hyper-eutrophic water body with HCBs. Six sampling ports (representing different layers) were evenly distributed along the water flow direction to study the purification processes of CWs. With HLRs ranging from 0.2 m/d to 0.8 m/d, total nitrogen (TN), total phosphorus (TP), COD, total suspended solid (TSS) and Chlorophyll a (Chl.a) were efficiently treated by CWs, and they were mainly removed at the second layer of CWs. The concentrations of two cyanobacterial metabolites (geosmin and β-cyclocitral) in the effluent were mostly below their odorous threshold concentrations. As the HLRs increased, the treatment efficiencies of the CWs decreased gradually. There was no removal of TP, Chl.a, geosmin, or β-cyclocitral at an HLR of 1.0 m/d. Under suitable HLRs, this type of CW could provide a promising way to control HCBs and associated odorous problems in hyper-eutrophic water bodies.