The general hydrotreatment catalyst is an alumina supported molybdenum sulfide catalyst which is usually promoted by cobalt and nickel. However, supported catalysts are easily deactivated because of a high portion of asphaltenes, which cause pore-plugging and mass transfer limitation. For this reason, recent studies are focused on unsupported nanocatalysts especially for slurry reactor application. To synthesize nanomaterials, generally, there are top-down methods such as sputtering and bottom-up methods using chemical precursors to synthesize nanomaterials. Since the synthesis of nanomaterials with complex chemical formulas is limited in the top-down method, the bottom-up method through liquid phase reaction is mostly used. However, in the case of nanomaterials produced in the liquid phase, a calcination process is sequentially needed in order to obtain the desired crystallinity and to remove impurities. Even if it succeeds in synthesizing uniform and nanosized materials in the liquid phase process, it is difficult to finally obtain nanomaterials due to particle growth by sintering between nanomaterials in the calcination process. This study presents a new synthetic approach of Ni-doped MoS2 nanoparticles via core shell nanoclusters, enabling control of the crystallization and the size of the target nanomaterials even after a high temperature calcination process. The Ni-doped MoS2 (Ni/Mo weight ratio = 0.45) nanoparticle exhibited the highest catalytic performance. The slab structures and surface oxidation states of the nanoparticles were investigated according to the amount of doped Ni through the analysis of TEM and XPS characteristics and also related to the catalytic performances of heavy oil upgrading.