VP2, the single outer protein of infectious bursal disease virus capsid, can self-assemble into T = 1 subviral particle (SVP), which can be efficiently purified by immobilized metal ion affinity chromatography (IMAC). In this study, a systemic investigation of the adsorption behavior of VP2 SVP on Ni-NTA resin was performed to identify that His253 and His249 on the surface of SVP are the key factors accounted for the strong and heterogeneous interaction. First, an untagged VP2-441 SVP was constructed, expressed, and purified by IMAC to demonstrate that SVP can interact with immobilized Ni2+ ions on NTA resin without an inserted His tag. Second, equilibrium adsorption studies were used to demonstrate that SVP has a higher affinity to the immobilized Ni2+ ions than a model protein, bovine serum albumin, although the maximum amount of SVP bound per volume resin is limited by the pore size of the resin as verified by confocal microscopic analysis. Third, based on structural analysis and computer modeling, His253 and His249 on the surface of SVP are responsible for a strong heterogeneous and multiple adsorption with the immobilized Ni2+ ions; and this was confirmed by a point-mutation experiment. This is the first example to elucidate the interaction between the immobilized metal ions and viral particles at molecular level. A detailed understanding of SVP-immobilized metal ion interactions can provide useful strategies for engineering icosahedral protein nanoparticles to achieve a simple and one-step purification by IMAC.