Whether crop intercropping can affect the uptake of phthalic acid esters (PAEs) by plant roots from soils is unclear. In this study, we compare the PAE uptake by plant roots between the wheat/maize intercropping and the wheat and maize monocropping in a field work. We show that the PAE bioconcentration factors of wheat and maize roots are remarkably higher under wheat/maize intercropping than under monocropping, indicating that intercropping may significantly increase the biouptake of PAEs as compared to monocropping. The wheat/maize intercropping can increase the electron transfer capacity (ETC) of water-extractable organic matter (WEOM) in soils by increasing the abundance of redox-active functional groups in WEOM. The ETC-enhanced WEOM may be an important reason for facilitating the reduction of ferric iron [Fe(III)] minerals to soluble ferrous iron (Fe(II)] by acting as electron shuttle, thus leading to the release of the PAEs originally occluded in Fe(III) minerals into soil pore water. The increased bioavailable PAEs distributed in the soil pore water under wheat/maize inter cropping eventually result in the increase in the uptake of PAEs by plant roots from soils. The results can provide insights into the link between the uptake of PAEs by crops and the cropping practices in agricultural ecosystems.