A well-defined test structure of organic static-induction transistor (SIT) having regularly sized nano-apertures in the gate electrode has been fabricated by colloidal lithography using 130-nm-diameter polystyrene spheres as shadow masks during vacuum deposition. Transistor characteristics of individual nano-apertures, namely 'nano-SIT,' have been measured using a conductive atomic-force-microscope (AFM) probe as a movable source electrode. Position of the source electrode is found to be more important to increase current on/off ratio than the distance between source and gate electrodes. Experimentally obtained maximum on/off ratio was 710 (at VDS = -4 V, VGS = 0 and 2 V) when a source electrode was fixed at the edge of gate aperture. The characteristics have been then analyzed using semiconductor device simulation by employing a strongly non-linear carrier mobility model in the CuPc layer. From device simulation, source current is found to be modulated not only by a saddle point potential in the gate aperture area but also by a pinch-off effect near the source electrode. According to the obtained results, a modified structure of organic SIT and an adequate acceptor concentration is proposed. On/off ratio of the modified organic SIT is expected to be 100 times larger than that of a conventional one.