In order to evaluate and improve multimodal molecular imaging technology, a three-dimensional anatomical model of a BALB/c mouse was developed based on micro-CT imaging with a liver-specific contrast agent Fenestra LC. By using image processing and interactive segmentation methods, we delineated some primary organs and tissues, including the skin, skeleton, muscle, heart, lung, liver and spleen. Finally, cone-beam x-ray CT and bioluminescence tomography simulation experiments demonstrate the availability and flexibility of the proposed mouse model.