Dual biocidal groups of N-halamine and pyridinium were used to modify surface of magnetic sub-microparticles to exert enhanced synergistic antibacterial capacity. Magnetic silica Fe3O4 sub-microparticles (SMPs) were synthesized and then encapsulated with interpenetrating polymer network (IPN) of polystyrene (PS) and poly (acrylic acid) (PAA). The carboxylic acid groups of PAA were used as surface reactive sites to bond with amino groups of 4-aminopyridine through amidation reaction. N-halamine/pyridinium-derivatized magnetic sub-microparticles were sequentially produced by quaternization of the pyridine to pyridinium with 1-chlorohexane and chlorination of amide N-H to N-halamine with NaClO. The synthetic steps and products were characterized with Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and X-ray photoelectron spectrocsopy (XPS). The N-halamine/pyridinium-derivatized SMPs with dual biocidal functionalities showed faster deactivation abilities against both Escherichia coll. and Staphylococcus aureus compared with their counterparts that contained only N-halamine or pyridinium, and exhibited promising stability toward repeated washing and long-term storage. The designed SMPs in this study offer potential and ideal candidates for sterilization application due to multiple advantages including improved synergistic biocidal ability, high surface area, and easy recyclability.