Hepatitis B core virus -like particle (HBc-VLP) has become a carrier for expression and presentation of foreign epitopes as vaccine candidates. Efficient purification is necessary for preparation of HBc-VLP and its derivatives with various foreign epitopes. In previous reports, HBc-VLP was mainly purified with ion exchange chromatography. In this study, we developed a platform purification technique based on hydrophobic interaction chromatography (HIC). The underlying principle is the strong hydrophobicity on the surface of HBc-VLP, which was found by mathematical calculation and experimental measurement. Based on HIC, a complete downstream process, from feedstock supernatant to the final pure product, was developed involving a heat pretreatment, an HIC, an ultrafiltration concentration and a size exclusion chromatography. The total recovery of HBc-VLP was 41.92% with nearly 100% purity. HIC was also applicable to three HBc-based vaccine candidates displaying epitope from nuclear protein (NP) and matrix protein 2 (M2e) of the influenza A virus, as well as from ovalbumin (OVA). Optimal HIC condition for these three recombinant VLPs was rationally designed by analysis on their surface hydrophobicity, which was influenced upon insertion of the foreign epitope. By applying the same process developed for HBc-VLP, satisfactory results were achieved for product recovery, purity and host cell DNA removal, thus it is possible to become a platform technique for various HBc-VLP based vaccine candidates.