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Micro-CT with a high spatial resolution in combination with computer-based-reconstruction techniques is considered a powerful tool for morphological study of insects. The quality of CT images crucially depends on the precise knowledge of the scan geometry of the micro-CT system. In this paper, we have proposed a method to calculate the deviation of rotating axis for compensating deficiency of existing methods. A practical application of this geometric calibration method of the micro-CT system for insect imaging is presented. We have performed the computer-simulation study and experimental study with our prototype micro-CT system. The results demonstrate that the proposed technique is accurate and robust. In addition, we have evaluated the imaging characteristics of the detector in terms of modulation-transfer function (MTF). Finally, insect imaging performance and image reconstruction from data acquired with different energies are presented.