Objective The three-dimensional (3D) solid model of medulla oblongata-upper cervical spinal cord based on specimen pathological section data was established, and the stress and strain levels of medulla oblongata-upper cervical spinal cord under dentate process compression were obtained by finite element analysis, so as to provide references for clinical research. Methods Mimics was used to process the slice data, so as to establish the point cloud model. SolidWorks was used to locate, edit and optimize the point cloud model, so as to establish the 3D solid model. HyperMesh was used to establish the finite element model and ANSYS was used for finite element analysis. Results The medulla oblongata-upper cervical spinal cord model with clear boundary between gray matter and white matter and white matter fiber bundle was established. The stress and strain levels and stress-strain curves of white matter and gray matter under different compression degrees were obtained. Conclusions Combined with pathological sections of specimens and reverse engineering, the 3D medulla oblongata-upper cervical spinal cord model with clear morphology and structure of gray/white matter can be established. When the medulla oblongata-upper cervical spinal cord is compressed, the stress level of gray matter is lower than that of white matter, and about 20% of compression is the critical state of white matter. When the disease develops beyond the critical state, the biomechanical properties of white matter may fail, resulting in gray matter damage.