Aiming to address the key challenges of poor enzyme stability, difficult recovery, and difficult synergistic optimization of catalytic efficiency in high-value conversion of biomass, this study utilizes mineralization self-assembly technology to combine laccase with Fe₃O₄@SiO₂-PMIDA-Cu²⁺ composite, constructing magnetic laccase nanoflower (MLac-NFs) materials with a porous structure and superparamagnetism. This synthetic material can efficiently catalyze the selective oxidation of 5-hydroxymethylfurfural (HMF) to 2,5-furandicarboxylic acid (FDCA). The characterization results indicated that MLac-NFs exhibit optimal catalytic activity (63.4 U mg⁻¹) under conditions of pH 6.0 and 40 °C, with significantly enhanced storage stability (retaining 94.26% of activity after 30 days of storage at 4 °C). Apparent kinetic analysis reveals that the substrate affinity and maximum reaction rate of MLac-NFs were increased by 38.3% and 439.6%, respectively. In the laccase–mediator system (LMS), MLac-NFs mediated by 30 mM TEMPO could achieve complete conversion of HMF to FDCA within 24 h. Moreover, due to the introduction of magnetic nanoparticles, the MLac-NFs could be recovered and reused via an external magnetic field, maintaining 53.26% of the initial FDCA yield after six cycles.