The toxicity grade for a bulk material can be approximately determined by three factors (chemical composition, dose, and exposure route). However, for a nanomaterial it depends on more than ten factors. Interestingly, some nano-factors (like huge surface adsorbability, small size, etc.) that endow nanomaterials with new biomedical functions are also potential causes leading to toxicity or damage to the living organism. Is it possible to create safe nanomaterials if such a number of complicated factors need to be regulated? We herein try to find answers to this important question. We first discuss chemical processes that are applicable for nanosurface modifications, in order to improve biocompatibility, regulate ADME, and reduce the toxicity of carbon nanomaterials (carbon nanotubes, fullerenes, metallofullerenes, and graphenes). Then the biological/toxicological effects of surface-modified and unmodified carbon nanomaterials are comparatively discussed from two aspects: the lowered toxic responses or the enhanced biomedical functions. We summarize the eight biggest challenges in creating low-toxicity and safer nanomaterials and some significant topics of future research needs: to find out safer nanofactors; to establish controllable surface modifications and simpler chemistries for low-toxic nanomaterials; to explore the nanotoxicity mechanisms; to justify the validity of current toxicological theories in nanotoxicology; to create standardized nanomaterials for toxicity tests; to build theoretical models for cellular and molecular interactions of nanoparticles; and to establish systematical knowledge frameworks for nanotoxicology.