A high resolution Micro-CT system for small animal imaging is introduced in this paper. Micro-focus X-ray tube with focal diameter of 100 microm and flat panel detector with imaging area of 13cm x 13cm are adopted in this system. The data acquired in rotation scanning is reconstructed with cone beam algorithm. The resolving power of the detector is measured to be 31 lp/cm at 10% of the MTF. The resolution of the Micro-CT system could achieve 185 m when the magnification factor is 1.94. Thighbone of a rabbit is used as sample imaging with the system. The trabecular bone could be imaged clearly. And the ability of small animal imaging of the system has been demonstrated.