Carbon nanomaterials have gained significant momentum as promising candidate materials for biomedical applications due to their unique structure and properties. After functionalization with magnetic and fluorescent components, the resultant carbon-based nanohybrids can serve not only as magnetic resonance and fluorescence imaging contrast agents, but also as photothermally/magneto-thermally responsive drug carriers for combined photothermo/chemotherapy. This mini-review summarizes the latest developments and applications and addresses the future perspectives of carbon-based magnetic and fluorescent nanohybrids in the biomedical field.