The finite difference time domain(FDTD) method was adopted for simulation of the conical bionic moth-eye micro-nano structure on silicon substrate in middle infrared band(3-5 μm). A parameter-optimized combination of the micro-nano structure which was of low reflection was obtained by analyzing the parameters of the micro-nano structure, such as fill factor, period and etching depth. In order to guide the actual processing better, tolerance analysis of different parameters was carried out. The binary exposure and reactive ion etching technology were applied to fabricate the conical bionic moth-eye micro structure on silicon substrate in processing. The surface topography of the micro structure was acquired by thermal field emission scanning electron microscopy. The test of the silicon wafer with single-sided micro structure polishing by the infrared imaging spectrometer demonstrates that the reflectivity of the bionic moth-eye micro structure vibrates approximately 5% in middle infrared band.