A one-step facile strategy is developed to prepare highly disordered MoS2-based monolayers via the thermal organometallic decomposition in the presence of elemental sulfur and oleylamine. Characterizations including TEM, SEM, XRD, Raman spectroscopy, XPS, and nitrogen adsorption-desorption confirm the monolayer structure of the MoS2-based sulfides with similar ultrasmall lateral sizes of 4.2-4.6 nm and the successful doping of Ni and Co atoms in MoNiS and MoCoS. Due to the abundant active sites enabled by the ultrafine monolayer structure, these sulfides exhibit significantly improved activity in the hydrodesulfurization (HDS) of thiophene and hydrodenitrogenation (HDN) of pyridine compared to the commercial multilayer MoS2. Rational comparison of these catalysts justified by almost the same size, morphology, specific surface area confirms the superior promoting roles of Co for the HDS while Ni for the HDN, and further demonstrates that pyridine is a competitive inhibitor for thiophene in binding to the active sites of the catalysts. Moreover, excellent reusability for five consecutive cycles in the HDS and HDN is exhibited by MoCoS and MoNiS, respectively, which is attributed to their well-retained monolayer structure during the tests. This study highlights the significance of advanced synthetic strategy for improving the catalytic performance of Mo-based sulfides as industrial HDS and HDN catalysts.