As common industrial raw materials, malachite green (MG) and Cr(Ⅵ) generally coexist in waste liquids discharged from the paper printing, leather, and textile industries, causing serious harm to humans and the environment. Therefore, developing an effective method for the synergistic removal of MG and Cr(Ⅵ) from aquatic environments is of great research value. In this work, the non-homogeneous Fenton-like catalysts, namely, EDDS-Silica and EDDS-Co2+-Silica were successfully prepared using ethylenediamine disuccinic acid (EDDS) and silica gel (Silica) as raw materials, and a non-homogeneous Fenton-like catalytic method was developed for the efficient and synergistic removal of MG and Cr(Ⅵ) from wastewater. EDDS-Silica and EDDS-Co2+-Silica were analyzed using Fourier infrared spectroscopy and X-ray photoelectron spectroscopy to determine their structural composition and elemental contents. The catalytic degradation and removal effects of these materials in an MG single-waste system were also investigated. The results demonstrated that the incorporation of both materials can overcome the limitation of the conventional Fenton reaction, which is its applicability to acidic environments only. Moreover, EDDS-Co2+-Silica showed better degradation effects on MG than EDDS-Silica. Quantitative calculations based on density functional theory were used to predict the optimal coordination forms between Co2+and EDDS-Silica as well as the MG structure. The lowest unoccupied and highest occupied molecular orbitals of the catalysts were then used to predict the active sites on which MG tends to capture or release electrons during the degradation reaction. The optimal conditions for the synergistic removal of MG and Cr(Ⅵ) from a binary system using EDDS-Co2+-Silica were further investigated under different influencing factors. The results showed that EDDS-Co2+-Silica still had excellent catalytic effect on the degradation rate of MG in the range of pH 3-7, and the optimal conditions were as follows: solution pH, 7; degradation time, 1 h; temperature, 25 ℃; H2O2 concentration, 20 mmol/L; and the initial mass concentration of Cr(Ⅵ), 25 mg/L. Under the above conditions, the degradation rate was increased from 87.25% to 96.67% compared with that in the MG monosystem. Obvious enhancements in degradation effect and efficiency confirmed that the incorporation of EDDS-Co2+-Silica was favorable for the synergistic removal of MG and Cr(Ⅵ) in the binary system. Strongly oxidizing Cr(Ⅵ) can participate in the Fenton reaction, thus promoting MG degradation over a wide pH range. Thus, a positive synergistic effect exists between MG and Cr(Ⅵ). Considering that a large number of metal ions remained in the solution after the degradation reaction, EDDS-Silica was added to the degradation solution, and adsorption experiments were performed for 4 h at 30 ℃to adsorb and remove Cr and Fe via the strong chelating property of EDDS. The total residual mass concentrations of Cr and Fe were 4.96 and 1.02 mg/L, respectively, which meet national emission standards. These findings indicate that EDDS-Silica has good effects on the removal of residual metal ions after the nonhomogeneous Fenton reaction. As heterogeneous Fenton-like catalysts, the aminopolycarboxylic acid-modified materials proposed in this study can simultaneously promote the Fenton reaction and remove residual metal ions, thereby effectively removing MG and Cr(Ⅵ) from the binary system while ensuring that the content of residual metal ions in the system meets environmental emission standards. This study has broad application prospects in dye degradation and heavy-metal-ion wastewater treatment, and provides a reference value and theoretical basis for the development of other similar ligand-modified materials.