We have proposed an effective method to synthesize and optimize multichannel fiber Bragg grating filters (MCFBGFs). The novel method contains two steps, i.e., the discrete layer peeling algorithm generates the excellent initial guess values and, successively, the nonlinear least squares method reconstructs and optimizes the expected fiber Bragg grating parameters from the initial guess in the previous step. Design examples demonstrate that the proposed method has unique merits to optimize the reflectivity and dispersion of MCFBGFs and effectively reduce their index modulation simultaneously.