The invention discloses a polypyrrole microelectrode with three-dimensional structure which belongs to the technical field of the micro-electro-mechanical preparation and is used in the miniature supercapacitor, and a preparation method thereof. The preparation method of the microelectrode comprises the following steps: adopting the MEMS technology to coat a SU-8 epoxy group negative chemically amplified resist on the surface of a copper substrate, performing spin-coating, pre-baking, lithographic process treatment, exposure, post-baking, development, rinsing and heat setting to form a columnar structure which is prepared from SU-8 photoresist and is in an array arrangement, on the surface of the copper substrate, and covering a functional film composed of polypyrrole and conductive material on the surfaces of the copper substrate and the microcolumn array microelectrode. The invention solves the problems that the common polypyrrole electrode with a two-dimensional structure can not store a large quantity of charges, have high internal resistance and the like, thus improving the energy storage characteristic and large current discharge performance of the miniature supercapacitor. The miniature supercapacitor of the invention has wide application prospect in the fields of sensor network node power supply, micro-robot driving power and fuze power.