In-vivosmall animal imaging system is an important part of disease research and new drug development. It is essential for living small animal imaging system to be able to provide the anatomical structure, molecular and functional information. The X-ray micro cone-beam computed tomography (micro-CBCT) can perform longitudinal study with a resolution of tens-to-hundreds of microns in a short imaging time at a relatively low cost. Furthermore, it is easy to combine with other modalities to provide abundant information about small animals. A key challenge to the micro-CBCT scanner is that its spatial and contrast resolution determined primarily by the X-ray focal spot size, the detector element size, and the system geometry. Aiming to improve the spatial resolution, contrast resolution, and imaging uniformity of the micro-CBCT system, we use the X-ray polycapillary optics for adjusting the X-ray source. A micro-CBCT based on X-ray polycapillary optics with a large field of view is constructed for the small animal imaging study. The micro-CBCT system is composed of microfocus X-ray tube with an attached polycapillary focusing X-ray lens, amorphous silicon-based flat panel detector, rotation stage, and controlling PC. The Feldkamp-Daivs-Kress (FDK) algorithm is adopted to reconstruct the image. The system performances are evaluated. The magnification of this micro-CBCT system is 1.97. The results show that the spatial resolution of the system at 10% modulation transfer function (MTF) is 9.1 lp/mm, which is 1.35 times higher than that in the case of no optics. The image uniformity deterioration caused by hardening effect is effectively alleviated by filtrating the low energy X-rays with the X-ray polycapillary optics and the contrast enhancement is more than twice. The anesthetic rats are imaged with this micro-CBCT system in vivoand the practicability of the system in small animal imaging research is verified.