In order to reveal the mechanisms of Fe-inhibited plant root growth and Zn-alleviating effects on iron (Fe) toxicity, wheat cultivars Xihan 4 seedlings were used to investigate the relationship between root growth and synthetic metabolism of lignin in response to 300 µM Fe stress alone or in combination with 50 or 250 µM zinc (Zn). Fe-alone-exposed roots exhibited significant increase of cell wall lignin content and the stimulation of phenylalanine ammonia-lyase (PAL), 4-coumarate:CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), laccase (LAC), cell wall bound guaiacol peroxidase activity (CW-bound GPX) and conifers alcohol peroxidase (CAPX) activities as well as the up-regulation of TaPAL, Ta4CL, TaCAD and TaLAC expression. In comparison with Fe stress alone, the presence of Zn effectively alleviated the changes of these parameters in Fe-treated roots. And also, the results of lignin staining in the root tissue were consistent with those of lignin detection in wheat seedlings under different treatments. Further study showed the increase of apoplastic hydrogen peroxide (H2O2) content in conjunction with the stimulation of CW-bound nicotinamide adenine dinucleotide (NADH) oxidase, plasma membrane (PM) nicotinamide adenine dinucleotide phosphate (NADPH) oxidase and apoplastic superoxide dismutase (SOD) in Fe-alone-stressed roots compared with untreated ones, but Fe + Zn treatment partially reversed the changes of these parameters in comparison with Fe exposure alone. Furthermore, the application of exogenous H2O2 not only enhanced the amount of cell wall lignin in Zn + Fe-treated roots but also significantly blocked Zn-alleviating effect on Fe-induced inhibition of root growth. In conclusion, the inhibition of root growth was associated with the increased accumulation of cell wall lignin in response to Fe exposure alone, which was due to the stimulation of lignin metabolizing enzymes and the up-regulation of related enzyme gene expression and the increase of apoplastic H2O2 generation in wheat roots under Fe exposure alone. It was also suggested that Zn-alleviating effect on Fe-induced inhibition of root growth might be related to the reduction of lignin content of root cell wall resulting from the decrease of apoplastic H2O2 content when wheat seedlings were exposed to Fe + Zn treatment.