Nanomaterials such as carbon nanotubes (CNT) can improve axonal connecting in a target direction during regeneration, however, it is limited by the neurotoxicity of CNT. Here we investigate the possible protective effect of nano-hydroxyapatite (n-HA) against nerve injury, as well as CNT in cultured rat cortical neurons. In this study the nanomaterials were characterized by X-Ray diffractometry (XRD) and atomic force microscopy (AFM) analysis. Our results showed that axonal migration and extension were increased significantly after n-HA treatment by immunocytochemistry assay. The patch clamp assay results showed that n-HA acts protectively after nerve injury, which inhibited the average amplitude and frequency of excitatory postsynaptic currents (EPSCs). n-HA is not neurotoxic for the electrophysiology activity of cells. To find the effect of n-HA on axonal guidance growth in the cultured cortical neurons, Netrin 1, one of the axonal guidance cues, was determined by RT-PCR and western blot assay. Compared to the control group, n-HA down-regulated the mRNA level of netrin 1, and moreover, the expression of netrin 1 decreased significantly in the cells. n-HA caused the axonal guidance growth to be mediated by netrin 1 during nerve regeneration. Therefore, the data from the present study provided a new approach for the therapy or prevention of nerve injury.