This paper reports the mechanism of two-photon absorption photopolymerization and the femtosecond laser technology used for biocompatible materials ORMOCER three-dimensional micro-nano processing.Two-photon absorption photopolymerization was achieved in ORMOCER resin, the resolution reached 0.5 μm less than the diffraction limitation. The mathematical expression of two photon photopolymerization threshold is derived, the effect of the scanning speed V and the laser power P on the transverse size is studied. Using two-photon femtosecond laser micro-processing technology fabricates a typical microbial devices such as micro-well array,micro-pole-array, and photonic crystal micro-biological scaffold.