A highly efficient Fenton-like catalyst was successfully developed by covalently immobilizing a Cu(II)–pyridine group complex onto silica microspheres. The catalyst was characterized by SEM, FTIR and XPS measurements. The catalytic activity was evaluated by heterogeneous degradation of Rhodamine B (RhB) with H₂O₂ in the dark. The effects of pH, catalyst loading, H₂O₂ concentration, initial dye concentration, and temperature on the degradation kinetics were investigated to optimize operational variables and find the potential mechanisms. It was found that the optimum pH of medium was near neutral, at which over 98% of RhB (5–7.5 mg L⁻¹) was efficiently decolorized in 6 hours with 2 g L⁻¹ catalyst and 200 mg L⁻¹ H₂O₂. The TOC removal of RhB (10 mg L⁻¹) also reached 72% after the reaction duration. Meanwhile, the acute toxicity of RhB to marine bacteria Vibrio fischeri was almost completely eliminated. The degradation of RhB could be well described with a pseudo-first order kinetic model. The reaction activation energy was approximately 38.60 kJ mol⁻¹. Fluorescence analysis and free radical scavenging experiments were performed, and revealed that the hydroxyl radical was the main active species for RhB degradation. The stability of the catalyst was confirmed by insignificant leaching of copper species and loss of activity after four cycles. Based on these results and the literature, a possible mechanism for RhB degradation was proposed.