Nanomaterials combined with antibiotics exhibit synergistic effects and have gained increasing interest as promising antimicrobial agents. In this study, vancomycin-modified magnetic-based silver microflowers (Van/Fe
3
O
4
@SiO
2
@Ag microflowers) were rationally designed and prepared to achieve strong bactericidal ability, a wide antimicrobial spectrum, and good recyclability. High-performance Fe
3
O
4
@SiO
2
@Ag microflowers served as a multifunction-supporting matrix and exhibited sufficient magnetic response property due to their 200 nm Fe
3
O
4
core. The microflowers also possessed a highly branched flower-like Ag shell that provided a large surface area for effective Ag ion release and bacterial contact. The modified-vancomycin layer was effectively bound to the cell wall of bacteria to increase the permeability of the cell membrane and facilitate the entry of the Ag ions into the bacterium, resulting in cell death. As such, the fabricated Van/Fe
3
O
4
@SiO
2
@Ag microflowers were predicted to be an effective and environment-friendly antibacterial agent. This hypothesis was verified through sterilization of Gram-negative
Escherichia coli
and Gram-positive methicillin-resistant
Staphylococcus aureus
, with minimum inhibitory concentrations of 10 and 20 μg mL
−1
, respectively. The microflowers also showed enhanced effect compared with bare Fe
3
O
4
@SiO
2
@Ag microflowers and free-form vancomycin, confirming the synergistic effects of the combination of the two components. Moreover, the antimicrobial effect was maintained at more than 90% after five cycling assays, indicating the high stability of the product. These findings reveal that Van/Fe
3
O
4
@SiO
2
@Ag microflowers exhibit promising applications in the antibacterial fields.