A bottom‐up methodology to fabricate a nanostructured material by Au nanoclusters on 6H‐SiC surface is illustrated. Furthermore, a methodology to control its structural properties by thermal‐induced self‐organization of the Au nanoclusters is demonstrated. To this aim, the self‐organization kinetic mechanisms of Au nanoclusters on SiC surface were experimentally studied by scanning electron microscopy, atomic force microscopy, Rutherford backscattering spectrometry and theoretically modelled by a ripening process. The fabricated nanostructured materials were used to probe, by local conductive atomic force microscopy analyses, the electrical properties of nano‐Schottky contact Au nanocluster/SiC. Strong efforts were dedicated to correlate the structural and electrical characteristics: the main observation was the Schottky barrier height dependence of the nano‐Schottky contact on the cluster size. Such behavior was interpreted considering the physics of few electron quantum dots merged with the concepts of ballistic transport and thermoionic emission finding a satisfying agreement between the theoretical prediction and the experimental data. The fabricated Au nanocluster/SiC nanocontact is suggested as a prototype of nano‐Schottky diode integrable in complex nanoelectronic circuits.