In Fluorescence Molecular Tomography (FMT), the reconstruction and fusion display of inner light source can be realized with the aid of CT data. A method is proposed in this paper to select permissible source region based on FMT image and CT data. The position and depth of light source can be estimated in FMT image. According to the coordinate relation of the two mode image, the light source position can be marked in CT data and mesh was produced on the marked CT data. Experimental results show that, the method can reduce the ill-posedness of the inverse problem and improve the accuracy of reconstruction of inner light source.