In this study, pot experiments of amaranth were carried out with phenanthrene-polluted soils separately mixed with nanoscale zero-valent iron (nZVI), nanoscale biochar (nBC) and nanoscale zero-valent iron biochar (nZVIBC) to investigate the effects of materials on soil physicochemical properties, amaranth physiological function and the migration and transformation of phenanthrene in soil-plant system. The results indicate that the application of nZVIBC increases the SOM to 1.38 times that of the control group and significantly increases non-desorbing fraction of phenanthrene (by 41.1%), while decreases roots bioconcentration factor of amaranth to phenanthrene (by 85.7%), which evidences the migration capability of soil phenanthrene is inhibited. Nevertheless, the addition of nZVIBC causes the residual amount of soil phenanthrene increase to 8.6 times that of material-free soil and increase the uptake and accumulation of phenanthrene in shoots and roots of amaranth by 42.9% and 37.9%, respectively. In addition, nZVIBC results in a raise of Fe content (42.0%) and a drop of Mn content (74.9%) in roots of amaranth, and finally reduces its fresh biomass significantly (55.8%), which is linked to the oxidative stress due to increased Fe and phenanthrene content. Two components in composite caused different effects, nZVI adversely affects the normal physiological function and antioxidant capacity of amaranth, while nBC induces alterations in SOM and phenanthrene content patterns. As a contamination remediation material of PAHs, nZVIBC effectively decreases the migration and transformation of soil phenanthrene and is suitable for in-situ chemical remediation of soil organic contamination.