To describe a simplified classification scheme for endplate injury morphology based on 3D CT and to examine possible associations between endplate injury morphology and vertebral space and other variables such as type of fracture and disc degeneration in a group of patients with thoracolumbar fractures. This study was a retrospective cohort study. We collected patients with thoracolumbar fractures admitted from January 2015 to August 2020 and divided them into three groups based on the morphology of endplate injury (45 cases of mild endplate injury, 54 cases of moderate endplate injury, and 42 cases of severe endplate injury, SEI). Data of vertebral body and intervertebral space height and angle, the Pfirrmann grade, endplate healing morphology were collected during preoperative, postoperative, and long-term follow-up of patients in each group. One-way analysis of variance (ANOVA), chi-squared test, and repeated measurement ANOVA were used to compare and analyze the influence of endplate injury morphology on patient prognosis. Most moderate injuries to the endplate (fissure-type injury) and severe injuries (irregular depression-type injury, Schmorl's node-type injury) resulted in significant disc degeneration in the long-term transition. This study also showed significant differences in the height of the anterior margin of the injured spine and the intervertebral space height index during this process. The current study suggests that although the region of injury in endplate fissure-type injury is small preoperatively, it may be a major factor in leading to severe disc degeneration, loss of intervertebral height, and Cobb angle in the long term. The results of our study therefore may allow surgeons to predict the prognosis of patients with thoracolumbar fractures and guide their treatment.