The correct orthogonality relation for optical fiber is applied to the perturbed coupled mode theory, and the corresponding coupled mode equations for common optical fiber are introduced. Its application to fiber Bragg gratings is discussed. The coupling coefficients of the equations for fiber Bragg gratings, being the distinguished feature for coupled mode theories, are different from other theories′. The solutions of the equations are discussed, and the simple formula between the peak reflectivity and the Bragg wavelength, the length of the fiber Bragg grating is obtained. An experiment of fiber Bragg gatings is completed. The peak reflectivity of the experiment is about 0.993, and the corresponding theoretical result is 0.999. The experimental result coincides with the theory very well.