The photo-polymerization induced by Two-Photon Absorption (TPA) is tightly confined in the focus because the efficiency of TPA is proportional to the square of intensity. Three-dimensional (3D) micro-fabrication can be achieved by controlling the movement of the focus. Based on this theory, a system for 3D-micro-fabrication with femtosecond laser is proposed. The system consists of a laser system, a microscope system, a real-time detection system and a 3D-movement system, etc. The precision of micro-machining reaches a level down to 700nm linewidth. The line width was inversely proportional to the fabrication speed, but proportional to laser power and NA. The experiment results were simulated, beam waist of 0.413μm and TPA cross section of 2×10-54cm4s was obtained. While we tried to optimize parameters, we also did some research about its applications. With TPA photo-polymerization by means of our experimental system, 3D photonic crystal of wood-pile structure twelve layers and photonic crystal fiber are manufactured. These results proved that the micro-fabrication system of TPA can not only obtain the resolution down to sub-micron level, but also realize real 3D micro-fabrication.