A novel design of antibacterial and magnetic halloysite nanotubes loaded with Ag and Fe3O4 was reported. In detail, magnetic nanoparticles (Fe3O4) were immobilized on the surface of halloysite nanotubes (HNTs) via electrostatic adsorption (termed as HNTs/Fe3O4). The magnetic HNTs/Fe3O4 was then modified by polydopamine to in-situ grow Ag nanoparticles by a redox reaction, forming a composite nanostructure of HNTs/Fe3O4@Ag. The HNTs/Fe3O4@Ag was incorporated into poly-l-lactic acid (PLLA) scaffold fabricated via selective laser sintering, with the intent to endow the scaffold with robust antibacterial function and favorable cell activity. The results showed that the released Ag+ from the scaffold significantly against E. coli activity, with bacterial inhibition rate above 99%. Moreover, ion release behavior showed a scaffold enable to sustain release Ag+ over 28 days. Furthermore, Fe3O4 nanoparticles constructed magnetic microenvironment greatly enhanced cell activity and promoted cell proliferation. In addition, tensile strength of the scaffold increased by 52.9% compared with PLLA scaffold. These positive results suggested that the HNTs/Fe3O4@Ag nanostructure possessed potential in facilitating bone repair.