Three novel stilbene derivatives (named as BPSBP,BESBP and BCSBP respectively) with D-π-D molecular motif, used as two-photon absorption (TPA) initiators, are designed and synthesized aimed at the excitation source of 800 nm. TPA induced photopolymerization behaviors are studied with the pumping of a femtosecond laser. Effects of the concentrations of TPA initiators on initiation thresholds and effects of the concentrations of TPA initiators, the polymerized energy and the exposure time on the resolution in polymerization are discussed in detail. 3D periodic microstructure with submicrometer resolution is fabricated and characterized by scanning elletron microscope (SEM) under optimized conditions using BPSBP as TPA initiators with the concentration of 32 μmol/g and polymerized energy of 9×105 mJ/cm2.