Fluorescence molecular tomography (FMT) plays an important role in studying physiological and pathological processes of small animals in vivo at molecular level. However, this technique suffers from relatively low spatial resolution. To complement the problem, there has been a strong demand for providing functional and morphological analysis at the same time. In this paper, we proposed a hybrid full-angle free-space FMT and X-ray micro-cone-beam computed tomography (CT) (micro-CBCT) prototype system, providing both functional and anatomical images. During the whole acquisition, the two subsystems acquire projection images (fluorescence and CT) synchronously to keep consistent body position without moving the animals. The acquired datasets are intrinsically coregistered in the corresponding coordinate and identified geometry. Tomographic fluorescence and CT images are reconstructed using normalized Born-based spatial regularization and Feldkamp-Davis-Kress methods, respectively. The experimental results of both phantom and in vivo mouse preliminarily validate the accuracy and performance of the integrated system.