An increasing number of patients are suffering from central nervous system (CNS) injury, including spinal cord injury. However, no suitable treatment is available for such patients as yet. Various platforms have been utilized to recapitulate CNS injuries. However, animal models and in vitro two-dimensional (2D)-based cell culture platforms have limitations, such as genetic heterogeneity and loss of the neural-circuit ultrastructure. To overcome these limitations, we developed a method for performing axotomy on an open-access three-dimensional (3D) neuron-culture platform. In this platform, the 3D alignment of axons in the brain tissue was recapitulated. For direct access to the cultured axons, the bottom of the 3D neuron-culture device was disassembled, enabling exposure of the neuron-laden Matrigel to the outside. The mechanical damage to the axons was recapitulated by puncturing the neuron-laden Matrigel using a pin. Thus, precise axotomy of three-dimensionally aligned axons could be performed. Furthermore, it was possible to fill the punctuated area by re-injecting Matrigel. Consequently, neurites regenerated into re-injected Matrigel. Moreover, it was confirmed that astrocytes can be co-cultured on this open-access platform without interfering with the axon alignment. The proposed open-access platform is expected to be useful for developing treatment techniques for CNS injuries.