Unlike the conventional scintillator coupled x-ray detectors, photon-counting-detectors have only photon noises. Therefore, it is believed to be play great roles in developing low-dose x-ray CTs. Photon-counting-detectors can discriminate the x-ray photon energy which can be greatly used for spectral CTs. Micro-CTs are now widely used for biomedical research using a small animal model and it makes possible to observe the physiological and pathological changes by taking high resolution 3D images without sacrificing it. In this study, we developed a micro-CT using a micro-focus x-ray tube and a photon-counting-detector to evaluate the use of the photon-counting-detector in a spectral CT or a low-dose CT. To compare the performance of the photon-counting-detector we also use a CMOS flat-panel-detector for the micro-CT imaging. Using the two types of micro-CTs, we took CT images of a phantom and compare system performances. The CT images taken by the photon-counting-detector had more severe ring artifacts and poor SNR but it has superior spatial resolution and higher contrast than CMOS flat-panel-detector. Although the photon-counting-detector is more susceptible to ring artifacts, we think the photon-counting-detector is worth further study for its application to the spectral-CT and low-dose CT.