In this work, an experimental study on compression properties of two E-glass 3D woven fabrics, known as integrally woven sandwich fabrics, has been presented. Compression properties of 2D face fabrics and the core, as structural parts of integrally woven sandwich fabric, have also been investigated. Compression behavior of the samples (compressibility, compression work, and compressive resilience) was analyzed from the aspect of the weave design of face fabrics and the core structure (shape and density of the pile yarns). Results of the investigation showed that “8” shaped core structure, the greater surface density of the pile yarns, and the less compact structure of face fabrics ensure better compression properties of 3D fabrics. Specific weave design of face fabrics and the structure of the core significantly influence the behavior of 3D fabrics during successive increases, followed by a gradual decrease of pressure. During the loading of 3D woven structures, three regions of curves can clearly be seen compared to two regions which are registered at 2D face fabrics. Concerning 3D woven fabrics, the first region represents compression of the core, the second region is prolonged core compression and the third region refers to the simultaneous compression of pile yarns in the core and face fabrics. The density of pile yarns plays an important role in the region 1. In region 2, both the shape and density of the pile yarns are significant. Influence of the weave of face fabrics on compression behavior of 3D fabric can be noticed to a lesser extent in the region 2 and, especially in the region 3, where highly packed yarns assemblies are created.