Display omitted •A new method was established to encapsulate silicon onto magnetic nanoparticles.•The silicon layer has better surface morphology, stronger acid resistance.•The purification result leaded to better results in comparison with commercial kit. A new method was developed for preparing monodisperse Fe3O4@SiO2 magnetic core-shell nanoparticles via three steps. The obtained nanoparticles exhibit high saturation magnetization, good surface topography and dispersion as characterized by FTIR, SEM and VSM. The experimental results of hydrochloric acid treatment show that the obtained nanoparticles have excellent acid resistance and stable and compact silicon coating. The magnetic core-shell nanoparticles were further tested for purification of plasmid DNA from E. coli DH5a cells. The result of purification leaded to better adsorption, elution and purity results in comparison with isolated commercial extraction kit.