Composite materials are widely used in various aircraft due to their high specific strength, stiffness, corrosion resistance, and robust design flexibility. However, when subjected to complex loading conditions, composite structures are susceptible to damage, necessitating prompt repair upon aircraft return. Analyzing the re-damage process of repaired structures is crucial for assessing aircraft structural reliability, lifespan, and determining whether a repeat flight is warranted. In this study, a prediction method was proposed for re-damage behavior through meso-modeling and energy analysis of the repaired composite bolted joint. First, this article established a meso-mechanical model for composite laminates, analyzed force transfer characteristics at the fiber − matrix interface, and derived equations for stress field. Additionally, a strain energy distribution model was developed for composite bolted repaired joint near fibers and repaired area, proposing a damage prediction method based on the strain energy criterion. This method could anticipate the location, type, sequence, and magnitude of damage. Finally, simulation calculations yielded mechanical characteristics of the repaired area under typical load conditions, while loading tests verified the feasibility of the prediction method. This study offered an effective means of predicting performance degradation in composite structures and provided a vital direction for optimal spacecraft structure repairing methods and parameters.