The invention provides a method for preparing a small-bore-diameter Si nanopore array template. The method comprises steps of magnetron sputtering, two-step anode oxidation, H3PO4 pore expansion and RIE pattern transfer. First, the final thickness of a Si slice-based AAO template can be controlled by adjusting the power and the time of the magnetron sputtering and the oxidation time of the first step of the two-step anode oxidation; the pore pitch and the pore diameter of the Si slice-based AAO template can be controlled by controlling the type of electrolyte in the two-step anode oxidation, electrolysis voltage and time of H3PO4 pore expansion; and the bore diameter of the Si template is reduced due to the final thickness of the AAO template by using the masking angle effect in the RIE pattern transfer process. Therefore, the bore diameter of the prepared Si nanopore array template can satisfy the requirement of small bores. The Si template prepared by the method can be widely applied to nano THz wave source devices, nano array field emission flat plate display devices, ferroelectric and ferromagnetic nano memory devices, nano light waveguide microelectronic and photoelectric devices and the like.