A fabricating method of Single Electron Transistor includes processing steps as follows: first, deposit the sealing material of gas molecule or atom state on the top-opening of the nano cylindrical pore, which having formed on the substrate, so that the diameter of said top-opening gradually reduce to become a reduced nano-aperture, whose opening diameter is smaller than that of said top-opening; then, keep the substrate in horizontal direction and tilt or rotate said substrate into tilt angle or rotation angle in coordination with tilt angle with the reduced nano-aperture as center respectively, and pass the deposit material of gas molecular or atom state through the reduced nano-aperture respectively. Thereby a Single Electron Transistor including island electrode, drain electrode, source electrode and gate electrode of nano-quantum dot with nano-scale is directly fabricated on the surface of said substrate.