Ultrasound (US) is a valuable tool for imaging soft tissue and visualizing tumor contours. Taking the benefits of US, we presented an integrated dual-modality imaging system in this paper that achieves three-dimensional (3D) bioluminescence tomography (BLT) with multi-view bioluminescence images and 3D US imaging. The purpose of this system is to perform non-invasive, long-term monitoring of tumor growth in 3D images. US images can enhance the accuracy of the 3D BLT reconstruction and the bioluminescence dose within an object. Furthermore, an integrated co-registered scanning geometry was used to capture the fused BLT and US images. We validated the system with an in vivo experiment involving tumor-bearing mice. The results demonstrated the feasibility of reconstructing 3D BLT images in the tumor region using 3D US images. We used the dice coefficient and locational error to evaluate the similarity between the reconstructed source region and the actual source region. The dice coefficient was 88.5%, and the locational error was 0.4 mm when comparing the BLT and 3D US images. The hybrid BLT/US system could provide significant benefits for reconstructing the source of tumor location and conducting quantitative analysis of tumor size.