A phase-contrast cone-beam computed tomography (PC CBCT) system is proposed for small-animal imaging that incorporates the in-line holography technique into CBCT system. Theoretical analysis shows that the in-line holographic image can be approximately transformed into line integrals of an object function composed of an attenuation term and a phase term. The Fresnel diffraction theory is applied to generate in-line holographic images along a circular orbit, and the Feldkamp-Davis-Kress algorithm is applied to reconstruct the object function. The proposed system was investigated using a numerical phantom, and the reconstruction was evaluated using the edge-enhancement factor and the relative reconstruction error. The reconstruction results show that all the structures in the numerical phantom are bounded with enhanced edges with negligible artifacts. These enhanced edges make the reconstruction visually sharper and clearer. The results show that while the relative reconstruction errors are very close to that of the conventional CBCT reconstruction, having a small cone angle, weak attenuation, small focal spot size, and high-resolution detector are preferred for a greater edge-enhancement effect.