Molybdenum disulphide nanostructures are of interest for a wide variety of nanotechnological applications ranging from the potential use of inorganic nanotubes in nanoelectronics to the active use of nanoparticles in heterogeneous catalysis. Here, we use atom-resolved scanning tunnelling microscopy to systematically map and classify the atomic-scale structure of triangular MoS2 nanocrystals as a function of size. Instead of a smooth variation as expected from the bulk structure of MoS2, we observe a very strong size dependence for the cluster morphology and electronic structure driven by the tendency to optimize the sulphur excess present at the cluster edges. By analysing of the atomic-scale structure of clusters, we identify the origin of the structural transitions occurring at unique cluster sizes. The novel findings suggest that good size control during the synthesis of MoS2 nanostructures may be used for the production of chemically or optically active MoS2 nanomaterials with superior performance.