One grand challenge of silicon-based microchannel plate (MCP) fabrication is to make the micro-pore array of high aspect ratio on the silicon wafer. Photo-assisted electrochemical etching technique is used to make such micro-pore arrays on n-type silicon substrate. Considering that the influences of matter transportation, solution concentration, illumination and temperature are reflected by the etching current and voltage under the actual etching conditions, the research is focused on the effects of the etching voltage and current on the morphology of the micro-pores. According to the structure and morphology of deep etching pores, the current, voltage and illumination are modified. Finally, the micro-pores of depth over 200 μm are fabricated on a 5 inch (1 inch=2.54 cm) silicon wafer. The large-area uniform pore array of high-aspect ratio is obtained. It meets the structure parameter requirements of MCP post-production.