The magnetic Fe3O4-SiO2 binary aerogel and nonmagnetic α-Fe2O3-SiO2 binary aerogels are obtained by adjusting the solvent type during the solvothermal reaction and varying the Fe/Si proportion in the sol-gel process. The microstructure, surface charge and the formation mechanism of iron-based silica binary aerogels are analyzed by SEM, zeta potential and BET. The influence of the Fe/Si proportion on the surface group and morphology of binary aerogels is also investigated by FTIR and TEM analysis. The adsorption behavior of the iron-based silica binary aerogels on the Congo Red (CR) dye is also discussed by adsorption kinetics model and adsorption isotherm model. In addition, the effects of pH and initial concentration of the solutions, adsorption time and the maximum adsorption capacities for CR of iron-based silica binary aerogels adsorbents are also discussed, respectively. Moreover, the maximum adsorption capacity of as-prepared magnetic Fe3O4-SiO2 binary aerogels for dyes achieved 489.13 mg g−1, the maximum adsorption capacity of nonmagnetic α-Fe2O3-SiO2 reached 454.55 mg g−1, respectively. Thus, the iron-based silica binary aerogels provides valuable clues for the study of other aerogel materials as adsorbents.