This study proposed the use of combined nano-sphere lithography (NSL) and photo-assisted electrochemical etching (PAECE) to generate arrayed nano-pillar with high aspect ratio on silicon wafer, and then used for the application of photonic crystals (PCs) Sensor. The experiment result indicates the NSL can conveniently define nano-array and PAECE technique can effectively yield nano-pores and nano-pillars. The nano-pore, depth of 2.3 μm and diameter of 90 nm, was generated by 1 V PAECE. When the bias of PAECE was enlarged to 2.2 V, nano-pillar array was produced with 2 μm in height, 100 nm in diameter and 201 for aspect ratio. The PCs sensor detection platform was composed by laser of 1550 nm, precision translation stage and polarimeter. Through this high sensitive system, we can examine the small bio-molecules of plasmid by means of the polarized variation represented in Poincarè sphere coordinate system.