In this paper, precise integration in a symplectic system is used to analyze the stop-band characteristic of the dielectric layer PBG structure in a waveguide. The transverse section is made discrete by using edge elements. The stiff matrices of a dielectric layer and an air layer can be calculated by precision integration based on Riccati equations in a Hamiltonian system. The export stiff matrices of a period can be obtained by a combination of substructures, and then the whole structure can be solved. The stop-band characteristic of a dielectric layer PBG structure in a waveguide is obtained and the effects of the size of period and the number of periods are discussed. The examples presented show that this method is precise and efficient.