Background and aims <p>Iron-modified biochar has been validated as an eco-friendly amendment for ameliorating saline-alkali soil. However, the mechanisms by which iron-modified biochar enhances plant growth in saline-alkali soil through the regulation of plant physiology and rhizosphere microecology remain unclear.</p> Methods <p>To investigate the mechanism of iron-modified biochar in promoting plant growth, a pot experiment was conducted with five treatments: CK (no biochar), 1% BC (pristine biochar), 2% BC, 1% BC@Fe (iron-modified biochar), and 2% BC@Fe.</p> Results <p>The dual-valent iron oxides with microscale sizes were loaded onto the surface of BC@Fe. Compared with BC, BC@Fe presented more functional groups, increased specific surface area, and lower zeta potential, which is conductive to ionic adsorption under alkaline conditions. Compared to CK, 2% BC@Fe application significantly increased cotton biomass by 3.9-fold, whereas 2% BC alone resulted in a 3.0-fold increase. Under the 2% BC@Fe treatment, Na⁺ content in leaves was reduced by 36.8%, while Fe content increased by 171.4%, thereby facilitating a higher photosynthetic rate and enhanced antioxidant enzyme activities. In addition, the 2% BC@Fe treatment decreased total soil salt content by 1.37-fold and increased soil nutrient availability. The improved soil properties induced by BC@Fe promoted the colonization of beneficial copiotrophs in the cotton rhizosphere. Furthermore, the 2% BC@Fe treatment enriched specific metabolites associated with the biosynthesis of benzoxazinoids and phenylpropanoids, and enhanced the interconnections between rhizosphere microbes and metabolites.</p> Conclusions <p>This study demonstrates BC@Fe as an effective material for alleviating plant salt-alkali stress and provides a novel strategy for improving saline-alkali soils.</p>