The Fe₃O₄–CuS@SiO₂ photocatalyst, synthesized via a multistep assembly technique, effectively degraded methyl orange (MO) dye in an aqueous solution under visible light irradiation. The solvothermal process generated Fe₃O₄–CuS nanoflowers, with Fe₃O₄ nanoparticles initially forming on the CuS surfaces. Subsequently, SiO₂ shells were applied to Fe₃O₄–CuS using the sol–gel technique, resulting in the synthesis of Fe₃O₄–CuS@SiO₂ photocatalyst. Within 20 min, the prepared photocatalyst demonstrated a remarkable MO degradation efficiency of 94 ± 0.07% and a sorption capacity of 81.30 mg g⁻¹. This efficacy was attributed to the synergistic effect between photocatalysis and adsorption. The superparamagnetic behavior of the catalyst at room temperature facilitated its high adsorbent recovery rate. The proposed MO degradation mechanism was discussed considering the effect of various parameters on sorption capacity. Langmuir isotherm modeling (R² = 0.9949) and excellent fitting using pseudo-second-order kinetics (R² = 0.9949) characterized the dye adsorption data. Thermodynamic assessment revealed that the sorption process is endothermic and spontaneous (∆H° = 110.0 kJ mol⁻¹, ∆G° = −3.03 to −14.80 kJ mol⁻¹, and ∆S° = 392.27 J mol⁻¹ K⁻¹). Notably, Fe₃O₄–CuS@SiO₂ maintained 78% ± 0.20% degradation efficiency after five sorption–desorption cycles for MO degradation, demonstrating its exceptional reusability. These findings underscore the superior environmental remediation potential of the Fe₃O₄–CuS@SiO₂ photocatalyst.