Nanoparticles entering biological systems or fluids inevitably adsorb biomolecules, such as protein, on their surfaces, forming a protein corona. Ensuing, the protein corona endows nanoparticles with a new biological identity and impacts the interaction between the nanoparticles and biological systems. Hence, the development of reliable techniques for protein corona isolation and analysis is key for understanding the biological behaviors of nanoparticles. First, this review systematically outlines the approach for isolating the protein corona, including centrifugation, magnetic separation, size exclusion chromatography, flow-field-flow fractionation, and other emerging methods. Next, we review the qualitative and quantitative characterization methods of the protein corona. Finally, we underscore the necessary steps to advance the efficiency and fidelity of protein corona isolation and characterization on nanoparticle surfaces. We anticipate that these insights into protein corona isolation and characterization methodologies will profoundly influence the development of technologies aimed at elucidating bionano interactions and the role of protein corona in various biomedical applications.