Provided is a method of fabricating a vacuum micro-structure, which is used for an element operating in a vacuum, the method comprising the steps of: (1) entirely etching an epitaxial layer of a silicon substrate having an SOI structure including an upper silicon epitaxial layer, an interlevel insulating layer and a lower silicon bulk layer to form two electrode structures and a floating vibratory structure, and encapsulating them with a vacuum sealing substrate in a vacuum; and (2) etching the silicon substrate having the SOI stricture from the back side to the interlevel insulating layer to open the electrode structures, and forming a metal electrode.