A new three-dimensional (3D) optical fluorescent tomographic imaging scheme is proposed with structured illumination and spatial Fourier-domain decomposition methods for the first time. In this spatial Fourier-decomposition optical fluorescence tomography (SF-OFT), the intensity of focused excitation light from an objective lens is modulated to be a cosine function along the optical axis of the system. For a given position in a two-dimensional (2D) raster scanning process, the spatial frequency of the cosine function along the optical axis sweeps in a proper range while a series of fluorescence intensity are detected accordingly. By making an inverse discrete cosine transformation of these recorded intensity profiles, the distribution of fluorescent markers along the optical axis of a focused laser beam is obtained. A 3D optical fluorescent tomography can be achieved with this proposed SF-OFT technique with a simple 2D raster scanning process.