In view of low imaging resolution and quantitative accuracy in fluorescence molecular tomography (FMT) which are caused by the assumption of homogeneous optical structural background, and considering that the “coarse-grain” diffuse optical tomography (DOT) methodology based on region-labeling (region-based DOT) presents a promising tool of in vivo reconstructing background optical structure with the aid of anatomical a priori, an approach of region-based DOT guided FMT reconstruction algorithm under continuous-wave mode is developed for improving sensitivity of FMT. Numerical simulations are conducted on a region-labeled three-dimensional (3D) digital mouse atlas. The reconstructed fluorescent yield image with optical structural a priori information provided by region-based DOT algorithm is compared with the results with accurate optical structural background and hypothetical homogeneous background, respectively, to investigate the performance of this method. Physical experiments on a phantom are also conducted to assess this methodology. Our simulated and experimental reconstruction results indicate that this region-based DOT guided FMT approach can significantly improve the sensitivity of FMT, as well as its imaging resolution and quantitative accuracy.