To date, various cancer nano-biomaterials have demonstrated success in preclinical studies, improving therapeutic outcomes, prolonging survival, and/or decreasing side effects. However, the translation from bench to bedside remains challenging. While a number of nano-biomaterials have entered clinical trials, only a few have been approved for clinical applications. Before the application of every nano-biomaterial, it is necessary to evaluate its biological toxicity and enable its safe use in patients. Further clinical trials are carried out under the premise of ensuring that the material exhibits low toxicity in vivo and in vitro. Here, we mainly focused on six types of nanomaterials (hollow mesoporous manganese oxides nanomaterials, titanium-based nanomaterials, graphene-based nanomaterials, two-dimensional theranostic nanomaterials, liposomal nanocarriers, metal-organic framework) and introduced their toxicity. Ultimately, we discussed the present challenges and future perspectives for the next stage of toxic research in nanomedicine.