In an effort to improve both the stability of virus-like particles (VLPs) and the medical activity of polyoxometalates (POMs), a new hybrid assembly system between human papillomavirus (HPV) capsid protein L1 and a europium-containing POM (EuW10) has been constructed, for the first time, via the electrostatic interactions between them. The co-assembly of EuW10 and HPV 16 L1-pentamer (L1-p) in buffer solution resulted in the encapsulation of POMs in the cavity of VLPs, which was further confirmed by cesium chloride (CsCl) gradient ultracentrifugation, SDS-PAGE, dynamic light scattering, and transmission electron microscopy, whereas the post-assembly of EuW10 with the as-prepared VLPs leads to the adsorption of POMs only on the external surface of particles, and both cases improved the thermal and storage stabilities of VLPs obviously. Particularly, the encapsulation of POMs in VLPs largely improved the antibacterial activity of EuW10, and thereby, the present study will be significant for both the stability improvement of protein vaccines and the development of POM medicine.