Carbon nanomaterials (CNMs), including fullerenes, carbon nanotubes, graphene, nanodiamonds and their derivatives, have been extensively used for biomedical applications, especially for cancer diagnosis and treatment. Most of these applications require covalent reactions to give the CNMs a high dispersibility in physiological environments, new biological functions for diagnosis and treatment, and tailored interactions with biological systems for efficient therapy. In this review, we summarize: the covalent bonding approaches to functionalize CNMs with polar surface groups, hydrophilic polymer layers, and bioactive molecules, and the specific surface chemistry that can prevent the interactions of CNMs with plasma proteins to suppress non-specific uptake and to enhance targeted uptake, aiming to advance the design of CNM-based therapeutics for precise theranostics.