Abstract: Carbon nanomaterials (fullerenes, graphene, carbon nanotubes, etc.) have broad application prospects in the biomedical and environmental fields due to their unique physicochemical properties. However, the research on the migration, transformation, and toxicity assessment of these materials in ecosystems and organisms is challenged by the interference of complex environmental matrices. The ¹³C labeling technique, with its advantages of high sensitivity, non-radioactivity, and no interference with the intrinsic properties of materials, has become an important tool in the study of nano-biological effects and safety. This article systematically reviews the application of ¹³C labeling technology in quantitatively tracking the migration process of carbon nanomaterials in animals, intestinal microorganisms, plants, and aquatic ecosystems. Meanwhile, it introduces the ¹³C skeleton labeling schemes of carbon nanomaterials and the exploration of their synthesis mechanisms. Additionally, this article summarizes the main challenges currently faced by this technology and looks forward to its future development trends.