In fluorescence molecular tomography (FMT), the reconstruction results can greatly benefit from a priori information of accurate tissue optical-structures, which is difficult to be obtained in vivo with the traditional diffuse optical tomography (DOT) alone. One of the solutions is to apply a priori anatomical-structures obtained with anatomical imaging systems such as X-ray computed tomography (XCT) to constrain the reconstruction process of DOT. However, since the X-ray imaging mechanism limits the contrast between soft-tissues, it is difficult to segment the abdominal organs from XCT images. In order to overcome the challenges, the anatomical-structures of a target mouse are approximately obtained through registering a standard mouse anatomical atlas, i.e., the Digimouse, to its XCT volume with non-rigid image registration, and the optical-structures of the target mouse is approximately estimated through anatomical-structures guided time-resolve DOT strategy. Results of numerical simulations reveals that the an effective target atlas can be obtained through the registration method, and the results show that the absorption and reduced scattering coefficients of each organs can be recovered with reasonable accuracies.