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The catalysis of Au thin film could be improved by fabrication of array structures in large area. In this work, nanoimprint lithography has been developed to fabricate flexible Au micro-array (MA) electrodes with ~ 100% coverage. Advanced electron microscopy characterisations have directly visualised the atomic-scale three-dimensional (3D) nanostructures with a maximum depth of 6 atomic layers. In-situ observation unveils the crystal growth in the form of twinning. High double layer capacitance brings about large number of active sites on the Au thin film and has a logarithmic relationship with mesh grade. Electrochemistry testing shows that the Au MAs perform much better ethanol oxidation reaction than the planar sample; MAs with higher mesh grade have a greater active site utilisation ratio (ASUR), which is important to build electrochemical double layer for efficient charge transfer. Further improvement on ASUR is expected for greater electrocatalytic performance and potential application in direct ethanol fuel cell.