The protruding (P) domain of the major capsid protein VP1 of norovirus (NoV) is the crucial element for immune recognition and host receptor binding. The heterologous P protein expressed by Pichia pastoris self-assembles into P particles. However, tag-free NoV protein purification schemes have rarely been reported due to the low isoelectric point of NoV proteins, which leads to highly competitive binding between the target protein and yeast host cell proteins at alkaline pH. In this study, a two-step purification scheme based on surface histidines and the charge on the NoV GII.4 strain P protein was developed. Using HisTrap and ion exchange chromatography, the P protein was directly purified, with a recovery of 28.1% and purity of 82.1%. Similarly, the NoV capsid protein VP1 was also purified using HisTrap and gel filtration chromatography based on native surface histidines and self-assembly ability, with 20% recovery and over 90% purity. Dynamic light scattering and transmission electron microscopy analyses of the purified NoV P revealed that most of these small P particles were triangle-, square- and ring-shaped, with a diameter of approximately 14 nm, and that the purified NoV VP1 self-assembles into particles with a diameter of approximately 47 nm. Both the purified NoV P and VP1 particles retained human histo-blood group antigen-binding ability, as evidenced by a saliva-binding assay.