In recent years, the application of Fluorescence Diffusion Optical Tomography (FDOT) technology in pre-clinical experiments is increasing. It is a non-invasive small animal functional image based on diffusion optical tomography (DOT), which uses photons to absorb and scatter the properties of different materials to reconstruct the structure of the small animal sections. Using this technology can reduce the amount of small animal used and accelerate the research courses from academic researches to clinical applications. However, the potential of this technique is currently limited by its poor spatial resolution. In this work, we develop a dual-modality imaging system combining three-dimensional (3D) fluorescence tomography with ultrasound (US) imaging. This design includes an electron-multiplying charge-coupled device (EMCCD), an ultrasound transducer and a fiber-coupled laser on a planar platform. A customized fluorescence/US system was used to reconstruct the 3D fluorescence tomography from optical surface images in position of the inclusions from US signals by using Near-Infrared Fluorescence and Spectral Tomography (Nirfast). Ultrasound B-mode imaging was used to obtain the structural information to precisely extract the tissue boundary of a sample and improve fluorescence reconstruction. The advantages of using this system are noninvasive, easy-to-use and good contrast to soft tissue. We validated the system with meat and a 4T1 tumor nude mice. From the FDOT image and the line profile, it can be seen that the edge information added to the ultrasound is sharper, and the soft tissue and the tumor can also get good results at the same time. The reconstruction results show the combined fluorescence/US system can effectively localize the tumor and drug metabolism. It is very helpful for the study of tumor location and the development of cancer drugs in the small animal study.