Silicon is one of important semiconductor materials in micro-fabrication technology. However it belongs to m3m point group, there is no second harmonic generation (SHG) in it. This is an obstacle for the integration of nonlinear micro-structures in optical system on chip. We present the silicon waveguide structure based on photonic crystals to realize SHG and overcome the technology bottle-neck. The configuration of waveguides and the basic principle are put forward. The computation model and methods based on finite difference time domain (FDTD) are given. Finally we present a design result aimed at the wavelength of 10.6 μm and analyze the SHG. The results show the enhancing electric quadrupole polarization leads to the SHG in silicon by virtue of photonic band edge effect. Under the condition of perfect phase matching, the conversion efficiency is 0.2% at the pumping power of 1.3 MW/mm2. At the end, effect factors of conversion efficiency are discussed briefly.