Abstract: The lattice sandwich structure with near-zero thermal warping characteristics has significant engineering application value in the field of thermal dimensional-stable structures for spacecraft. This type of structure is composed of a large number of micro-structural units and is usually fabricated by metal additive manufacturing technology. However, due to non-negligible geometric deviations caused by the manufacturing process of the additive manufacturing micro-structural units, there are significant differences between the actual vibration behavior of the structure and the designed performance. Therefore, it is urgently necessary to propose a vibration behavior prediction method for near-zero thermal warping sandwich structures considering the geometric size defects of additive manufacturing. Based on CT scanning technology, the geometric size defect characteristics of the additive manufacturing near-zero thermal warping sandwich structure were obtained, and a finite element model including manufacturing defects was established. The vibration behavior of the near-zero thermal warping sandwich structure under three orthogonal direction excitations was predicted. Compared with the finite element analysis results of the ideal model, the prediction errors of the finite element analysis results based on the reconstructed model and the experimental results were reduced by 50.18%, 53.66%, and 81.48%, respectively. The results show that this technology can be used for the service performance evaluation of near-zero thermal warpage sandwich structures in spacecraft and provides a quantitative analysis approach for vibration deformation for on-orbit remote sensing satellites.