Fabricating large-scale nanoarrays is a significant and challenging work in the field of nanometer devices. Anodic aluminum oxide (AAO) membrane is considered as a promising mask due to its inherent advantages such as low-cost and tunable pore diameter. However, there are few reports on the use of non-through-hole large-area AAO membrane as a mask. Due to its higher mechanical strength, non-through-hole AAO membrane has the advantage of self-supporting for large-area fabrication. Herein, we present a robust approach to transferring nanopattern to substrates with high fidelity by using the non-through-hole AAO membrane as an etching mask. A novel two-step inductively coupled plasma (ICP) etching method is adopted. The morphological evolution of the AAO during ICP etching is systematically investigated. The aspect ratio of the AAO can be quantitatively controlled by adjusting etching time. The AAO nanopore arrays with an area of 7.1 cm2 are successfully transferred to gallium nitride wafer to enhance photoluminescence. The luminous intensity of the nano-array LED with a pore diameter of 400 nm and a depth of 150 nm is improved by 3.4 times compared with the LED without the nano-array. This method extends the opportunities for AAO mask to serve as generic templates for novel applications that are previously impractical due to the difficulty of large-scale nano-pattern transfer.