A 3D measurement system based on the combination of image bundles and binocular structured light was proposed. It could measure the three-dimensional shape of small objects under the environment of detonation and impact, which could not be directly measured. The structured light was directly projected onto the surface of the measured object and the distorted fringe images were imaged to the front side of the image bundles. Then those images were collected into the camera by another imaging lens after transmitted to the other side of the image bundles. The height of the measured object could be reconstructed by the binocular matching as long as the corresponding phase distributions were restored by the three-frequency phase unwrapping algorithm. The experimental results show that the measuring system via image bundles can fulfill the 3D morphology reconstruction of the small objects with high precision and can bring the advantages of flexibility due to the introduction of image bundles.