A novel theory, namely, Fourier mode coupling (FMC) theory for fiber Bragg gratings (FBGs) is proposed in this paper. During analyzing coupled modes of FBGs, the Fourier transform relations among the amplitude coefficients of coupled modes are found for the first time. The general expressions of reflective and transmissive spectra of FBGs are deduced from the combination of Fourier transform with the well-known coupled-mode theory. In the proposed FMC theory, the spectral characteristics of the FBG are achieved by the calculation of coupled modes in the spatial domain spectrum, which is the Fourier transform result of refractive index perturbation in the FBG. The FBG spectrum based on the FMC theory is simulated here, and compared with those obtained from the coupled mode theory and pure Fourier transform. The comparison shows that the FMC theory for and the derived spactra of FBGs are in accordance with the coupled mode theory and the practical spectra of the FBG respectively. The FMC theory has many features, these being simple, clear, direct, accurate and fast, which could be used as a universal tool for fast spectrum analysis of any FBG with an arbitrary distribution of refractive index perturbation along the fiber axis.