We report that the birefringence of the polarization convertor in silicon-on-Insulator channel waveguide could be enlarged using photonic crystals. The photonic crystals consist of etched air holes shifted to the center of the waveguide. The polarization rotation due to the asymmetric modes in the shifted photonic crystal structure is investigated. The result shows that the length to convert 100% input light to the orthogonal polarization could be as short as 3.4 μm. The device can be used in the integrated optical quantum computing system.