Nanomaterials are widely used in commercial products, resulting in the release of nanoscale particles into the environment. This raises concerns about their potential exposure risks in complex biological matrices. Most attempts use engineered nanomaterials (ENMs) to mimic the biological behavior of nanoparticles in the environment, and labeling of ENMs by sensors is a commonly used approach for sensitive detection and tracking of ENMs in organisms. However, due to the distinct physicochemical properties of nanoparticles, different labeling approaches have been developed, each with varying applicability. In this Review, we summarize the three main types of labeling methods used for nanoparticles: fluorescent, radiological, and metallic labeling. We discuss their labeling mechanisms, efficiency, stability, target nanoparticles, and applicability in different organism models. Finally, we propose a labeling scheme for specific nanoparticles. Overall, this Review provides a comprehensive overview of the advances in nanoparticle labeling techniques and their potential applications in environmental and health studies.