Photonic crystals are periodic arrangement made of artificial microstructures, different from the refractive index of the material and the medium, thereby causing periodic changes in different structures. This paper will be a photonic crystal Crystal Wave Version 3.2 software design tool for system simulation, numerical bandgap diagram of photonic crystals with different structural test results are analyzed differences. The main research in silicon substrate filled PDMS its numerical simulation at a fixed material, calculate the size of the diameter and spacing of different angles to find the preferred range of the energy gap. Then remove the defect formation portion boules, into a variety of different waveguide and resonator structure and calculate the filter characteristics of the various structures, the future is expected to be applied to different elements of the optical system.