We have applied projection X-ray microscope for three- dimensional (3D) structure analysis by means of cone-beam computed tomography. The projection images of small insect, Omiscus Porcellio, were recorded in every 1 degree for whole direction (360 degree) with a stepping motor controlled sample rotator. The images were recorded with cooled CCD camera (HAMAMATSU C4880) which detect X-ray directly. The 3D image was reconstructed from cone-beam projections using back-projection algorithm. The resolution of the reconstructed 3D image (256 x 256 x 256 pixels) was about 20 micrometers . The digestive organs were clearly visualized in 3D.