A novel core@double-shell magnetic microsphere Fe3O4@SiO2@7MgO·2B2O3·7 H2O (Fe3O4@SiO2@MBH) for the efficient adsorption of congo red (CR) was successfully synthesized. Subsequently, a CR-functionalized sample (Fe3O4@SiO2@MBH-CR) was prepared for methylene blue (MB) and Cu(II) removal from wastewater. Through techniques such as X-ray diffraction, X-ray photoelectron spectroscopy, transmission electron microscopy, scanning electron microscopy, vibrating sample magnetometer, etc., the chemical composition, physical characteristics, and magnetic properties of ferromagnetic composite particles were identified. Many important factors, including pH, adsorption period, and elution characteristics, were evaluated and then adjusted accordingly. The highest concentration of adsorption for CR was approximately 332.53 mg g−1 under ideal conditions, indicating a higher adsorption capacity. Fe3O4@SiO2@MBH-CR exhibited significantly higher adsorption capacities compared to other known adsorbents, removing 408.51 mg g−1 for MB and 63.26 mg g−1 for Cu(II) through electrostatic attraction. Consequently, the Freundlich isotherm framework and the pseudo-second-order kinetic framework explained the adsorption kinetics and isotherm data, respectively. It is essential to remember that an external magnet facilitated the easy removal of adsorbents from a water-based solution. The potential adsorption mechanism was briefly explored, and our findings suggest that the new adsorbent Fe3O4@SiO2@MBH is a promising candidate for enhancing dye and Cu(II) adsorption capabilities from aqueous solutions.