Supported MoS2 nanoparticles constitute the active component of the important hydrotreating catalysts used for industrial upgrading and purification of the oil feedstock for the production of fossil fuels with a low environmental load. We have synthesized and studied a model system of the hydrotreating catalyst consisting of MoS2 nanoclusters supported on a graphite surface in order to resolve a number of very fundamental questions related to the atomic-scale structure and morphology of the active clusters and in particular the effect of a substrate used in some types of hydrotreating catalysts. Scanning tunneling microscopy (STM) is used to image the atomic-scale structure of graphite-supported MoS2 nanoclusters in real space. It is found that the pristine graphite (0001) surface does not support a high dispersion of MoS2, but by introducing a small density of defects in the surface, highly dispersed MoS2 nanoclusters could be synthesized on the graphite. From high-resolution STM images it is found that MoS2 nanoclusters synthesized at low temperature in a sulfiding atmosphere preferentially grow as single-layer clusters, whereas clusters synthesized at 1200 K grow as multilayer slabs oriented with the MoS2(0001) basal plane parallel to the graphite surface. The morphology of both single-layer and multilayer MoS2 nanoclusters is found to be preferentially hexagonal, and atom-resolved images of the top facet of the clusters provide new atomic-scale information on the MoS2−HOPG bonding. The structure of the two types of catalytically interesting edges terminating the hexagonal MoS2 nanoclusters is also resolved in atomic detail in STM images, and from these images it is possible to reveal the atomic structure of both edges and the location and coverage of sulfur and hydrogen adsorbates.