We report a novel imaging technique for fluorescence diffuse optical tomography (FDOT). Unlike conventional FDOT, this technique separates the imaging procedure into two steps to respectively reconstruct the structural information (such as the center position and the radius), and the functional information (such as the fluorophore concentration and/or lifetime) of a fluorescing target embedded in a turbid medium. The structural parameters of the target were estimated from the amplitude ratio and phase difference of fluorescence signals received at different detectors, because the amplitude ratio and phase difference were found independent of, or weakly related to, the functional parameters. Based on the estimated structural parameters, a dual-zone mesh technique was utilized to reconstruct the fluorophore concentration. Results of simulations and phantom experiments showed that the structural parameters could be accurately recovered, without knowing the functional information, and that the reconstruction accuracy of the functional parameter was greater than 80%.