Heavy ion beams with high linear energy transfer exhibit more beneficial physical and biological performance than conventional X-rays, thus improving the potential of this type of radiotherapy in the treatment of cancer. However, these two radiotherapy modalities both cause inevitable brain injury. The objective of this study was to evaluate the effects of heavy ion and X-ray irradiation on the cytoskeleton and cytomechanical properties of rat cortical neurons, as well as to determine the potential mechanism of neuronal injury after irradiation. Cortical neurons from 30 new-born mice were irradiated with heavy ion beams at a single dose of 2 Gy and X-rays at a single dose of 4 Gy; subsequent evaluation of their effects were carried out at 24 hours after irradiation. An immunofluorescence assay showed that after irradiation with both the heavy ion beam and X-rays, the number of primary neurons was significantly decreased, and there was evidence of apoptosis. Radiation-induced neuronal injury was more apparent after X-irradiation. Under atomic force microscopy, the neuronal membrane appeared rough and neuronal rigidity had increased. These cell changes were more apparent following exposure to X-rays. Our findings indicated that damage caused by heavy ion and X-ray irradiation resulted in the structural distortion and rearrangement of the cytoskeleton, and affected the cytomechanical properties of the cortical neurons. Moreover, this radiation injury to normal neurons was much severer after irradiation with X-rays than after heavy ion beam irradiation. Heavy ion beams with high linear energy transfer exhibit more beneficial physical and biological performance than conventional X-rays, thus improving the potential of this type of radiotherapy in the treatment of cancer. However, these two radiotherapy modalities both cause inevitable brain injury. of this study was to evaluate the effects of heavy ion and X-ray irradiation on the cytoskeleton and cytomechanical properties of rat cortical neurons, as well as to determine the potential mechanism of neuronal injury after irradiation. Cortical neurons from 30 new-born mice were irradiated with heavy ion beams at a single dose of 2 Gy and X-rays at a single dose of 4 Gy; subsequent evaluation of their effects were carried out at 24 hours after irradiation. An immunofluorescence assay showed that after irradiation with both the heavy ion beam and X-rays, the number of primary neurons was significantly decreased, and there was evidence of apoptosis. Radiation-induced neuronal i Under atomic force microscopy, the neuronal membrane have rough and neuronal rigidity had increased. These cell changes were more apparent following exposure to X-rays. Our findings pointed that damage caused by heavy ion and X- ray irradiation resulted in the structural distortion and rearrangement of the cytoskeleton, and affected the cytomechanical properties of the cortical neurons. Moreover, this radiation injury to normal neurons was much severer after irradiation with X-rays than after heavy ion beam irradiation.