To study the three-dimensional (3D) morphological evolution of damage of the polymer bonded explosive (PBX) during compression process, the damage process of the PBX at the mesoscopic scale was analyzed. Furthermore, the damage evolution of the PBX was also deduced. The 3D deformation behavior and devolution of the internal microstructure of PBX during the in situ compression process were systematically investigated by integrating micro computed tomography (CT) imaging and digital volume correlation (DVC) method. The displacement and strain inside the PBX during the loading of down load were obtained through the DVC method. The results revealed that the strain concentration always appeared at binders between the granules before failure and led to granule internal cracking or granule edge cracking. The results further indicated that integration of micro CT and DVC technique can provide a more practical and effective method for investigating the structural features, strain, and damage mechanism of PBXs during compression process. This study has significant meaning for comprehensive investigation of the damage mechanical behavior of PBX.