The invention belongs to the technical field of micronanometer manufacturing, relating to a method for electric discharge machining of micronanometer three-dimensional structure of a nanowire or a nanotube, comprising: (1) sticking a conductive nanowire or nanotube to a tungsten tip; (2) putting an electrode clamping device onto a displacement table, and controlling the movement of the displacement table via a multi-axis motion controller; (3) putting conductive material workpieces to an X/Y precision displacement table, and controlling the movement of the X/Y precision displacement table by the multi-axis motion controller; (4) connecting the cathode of a pulse power supply to the tungsten tip, and connecting the anode to the workpiece; (5) using an industrial personal computer to send orders to the multi-axis motion controller, controlling the displacement table provided with the electrode clamping device, providing working voltage for electric discharge machining by the pulse powersupply, collecting electric discharge gap voltage by a gap voltage detection device, and controlling the movement of an electrode feeding displacement table by the industrial personal computer according to gap voltage. The invention ensures that the size of electric discharge machining reaches the micrometer level and the nanometer level and simultaneously solves the problem of chip removal in themachining process.