Tunnelling spectroscopy with simultaneous transmission electron microscopy (TEM) was applied to an Fe-MgO composite film in which the Fe nano-particles were sandwiched by two thin MgO layers and nanometer-scale double-barrier tunnel junctions were formed. Using a movable needle-shaped electrode, nano-regions were selected and the geometry of the particle system was deformed. The real-time and simultaneous experiments of the deformation, the tunnel measurement and the TEM observation made it possible to confirm the condition under which the Coulomb staircase clearly appears. The measured staircase period corresponded approximately to the value estimated from the geometry observed by TEM. Thus, the feasibility of this method was verified.