Upon entering biological environments, nanomaterials rapidly adsorb ambient proteins, forming a “protein corona,” which profoundly influences their recognition, distribution, metabolism, and ultimate biological fate within organisms. This report will introduce our overall research strategy, leveraging AI methodologies to investigate the interactions among nanomaterials, biological systems, and the environment. We will highlight recent advancements in the construction of protein corona datasets and the development of foundational models. Furthermore, the report will briefly outline our work on model interpretability and knowledge consistency within the AI for Science (AI4Science) framework and share our reflections on the potential of AI researchers in scientific discovery.