Two-photon photopolymerization (TPP) with femtosecond laser is a promising method to fabricate three-dimensional (3D) photonic crystals (PCs). Based on the TPP principle, the micro-fabrication system has been built. The 3D woodpile PCs with rod space of 2000 nm are fabricated easily and different defects are introduced in order to form the cross-waveguide and the micro-laser structure PCs. Simulation results of the optical field intensity distributions using finite-difference time domain (FDTD) method are given, which support the designs and implementation of the PC of two types in theory.