The invention relates to a method for preparing an amorphous alloy surface microstructure by the coupling technology of pre-indentation and polishing, and belongs to the field of material surface microstructure machining. The method comprises the steps that an indentation test instrument is used for carrying out an array indentation test on an amorphous alloy surface subjected to polishing to forma pre-indentation array with specific shapes and size parameters; then chemical mechanical polishing is carried out on the amorphous alloy surface containing the pre-indentation array by utilizing apolishing solution, and in the process, the pre-indented area can promote the aggregation of polishing particles to enhance removing of materials in the area so that the microstructure with the nano-scale depth can be formed on the amorphous alloy surface; and then the surface subjected to polishing is cleaned by using acetone so that the micro-structured amorphous alloy surface can be obtained. According to the method, the pre-indentation parameters and the polishing process parameters are changed so that the microstructures with different structural shapes and parameters can be prepared conveniently and rapidly, and the method has a good application prospect in the fields of micro-nano optics, moulds, microfluidics, biomedicine, self-assembly, bionic surface science and the like.