<p>Hydroponic experiments and computational simulations were conducted to investigate the changes in the gene expression, structure, and binding mode of the rice transporter protein OsTIL to OPEs by the presence of Cd²⁺ and Zn²⁺. OPEs and Zn²⁺ were observed to promote seedling growth and OPEs alleviated the suppressive effect of Cd²⁺ on seedlings. Usually, Cd²⁺ and Zn²⁺ inhibited the accumulations of OPEs in plants accompanied by the decrease of RCF (root concentration factor) and TF (transport coefficient). In particular, Zn²⁺ promoted TDCPP accumulation only in roots accompanied by the increase of RCF and the decrease of TF. Furthermore, Cd²⁺ and Zn²⁺ affected the gene expressions of OPEs transporter-OsTIL response in the accumulation of OPEs in both single and compound pollution. After molecular dynamics simulation analysis, RMSD of the&#xa0;protein backbone, binding pocket, and ligand only in TDCPP-OsTIL complex also were significantly affected by two metal ions. Furthermore, two metal ions can press the interaction of OPEs and OsTIL by reducing the&#xa0;stability of protein structure and the numbers of HB (hydrogen bonds) and enlarging the&#xa0;pocket. However, Zn²⁺ extra supports an enlarged entrance for TDCPP, which could facilitate the entry of the coordination complex of Zn²⁺ with TDCPP into the pocket and improve TDCPP capacity of OsTIL.</p>