Fluorescence molecular tomography (FMT) is an emerging tool in the observation of diseases. A fast and accurate surface reconstruction of the experimental object is needed as a boundary constraint for FMT reconstruction. In this paper, an automatic, noncontact, and 3-D surface reconstruction method named 360◦ Fourier transform profilometry (FTP) is proposed to reconstruct 3-D surface profiles for FMT system. This method can reconstruct 360◦ integrated surface profiles utilizing the single-frame FTP at different angles. Results show that the relative mean error of the surface reconstruction of this method is less than 1.4% in phantom experiments, and is no more than 2.9% in mouse experiments in vivo. Compared with the Radon transform method, the proposed method reduces the computation time by more than 90% with a minimal error increase. At last, a combined 360◦ FTP/FMT experiment is conducted on a nude mouse. Not only can the 360◦ FTP system operate with the FMT system simultaneously, but it can also help to monitor the status of animals. Moreover, the 360◦ FTP system is independent of FMT system and can be performed to reconstruct the surface by itself.