In combination of direct phase retrieval of coherent x-ray diffraction patterns with a novel tomographic reconstruction algorithm, we, for the first time, carried out quantitative 3D imaging of a heat-treated GaN particle with each voxel corresponding to 17 x 17 x 17 nm3. We observed the platelet structure of GaN and the formation of small islands on the surface of the platelets, and successfully captured the internal GaN-Ga2O3 core shell structure in three dimensions. This work opens the door for nondestructive and quantitative imaging of 3D morphology and 3D internal structure of a wide range of materials at the nanometer scale resolution that are amorphous or possess only short-range atomic organization.