The extent to which, and mechanisms by which, arbuscular mycorrhizal fungi (AMF) and additional aeration (AA) purify wetlands polluted by combined heavy metals (HMs) are not well understood. In this study, vertical flow constructed wetlands (VFCWs) with the Phragmites australis (reeds)-AMF/AA were used to treat combined HMs-polluted wastewater. The results showed that (1) AA improved the AMF colonization in VFCWs, and AMF accumulated the combined HMs in their structures; (2) AMF inoculation and/or AA significantly promoted the reeds growth and antioxidant enzymes activities, thereby alleviating oxidative stress; (3) AMF inoculation and AA significantly enhanced the removal rates of Pb, Zn, Cu and Cd under the stress of high combined HMs concentrations comparing to the CK treatment (autoclaved AMF inoculation and no aeration), which increased by 22.72%, 30.31%, 12.64%, and 50.22%, respectively; (4) AMF inoculation and/or AA significantly promoted the combined HMs accumulation in plant roots and substrates, and altered the distribution of HMs at the subcellular level. We therefore conclude that AMF inoculation and/or AA in VFCWs improves the purification of combined HMs-polluted wastewater, and the VFCWs-reeds-AMF/AA associations exhibit great potential for application in remediation of combined HMs-polluted wastewater.