Disclosed is an X-ray tube system with a disassembled carbon nanotube substrate for generating micro focusing level electron beams. A housing provides a vacuum space. An anode forms an electric field by a voltage applied from the outside and accelerates the electrons emitted from the cathode to reach the anode itself. A carbon nanotube substrate used as a cathode corresponding to the anode. A cathode plate supports and fixes the carbon nanotube substrate and applies a voltage to the carbon nanotube substrate. A sample probe is installed assemblably/disassemblably in the housing. A grid electrode is installed in front of the carbon nanotube substrate and extracting electrons from the carbon nanotube substrate in an easy manner. An electron focusing lens focuses the electrons passed through the grid electrode to form a micro level focus in the anode. A feed through applies a voltage to the cathode, the grid electrode and the electron focusing lens. A vacuum pump sustains a vacuum state inside the housing in exchanging the carbon nanotube substrate. A vacuum valve isolates the inside from the outside of the housing when the sample probe is inserted into the housing and disassembled from the housing.