In this research, a highly active unsupported MoS2 quantum dots (M-QDs) nanocatalyst was synthesized through exfoliation and dispersion of MoS2. In this research, an easy, low-cost, high yield, and scalable method is presented and performed as a single step as a nanocatalyst for hydrodesulfurization (HDS). The catalysts were characterized by XRD, FESEM, AFM, Raman Spectroscopy, UV-vis Spectroscopy, Florescence Spectroscopy, BET-BJH, TPR, and NH3-TPD analyses. XRF spectrometry technique was used to measure the sulfur of the feed and products. The HDS reactions of M-QDs nanocatalyst were investigated under different operating parameters. The conversion of the HDS of naphtha with 2500 ppm of sulfur indicated a noticeably higher yield of unsupported MQDs nanocatalyst (0 ppm Sulfur) as compared with the Co-Mo/gamma Al2O3 as a commercial catalyst which is economically valuable. DFT results revealed that the defected MoS2 structure provides a weak adsorption affinity toward hydrogen on Mo sites which could also dissociate the H-2 molecules through an endothermic reaction. It can be stated that the sulfur-defected MoS2 structure is more favorable to perform the HDS reaction which can be due to activation of H-2 molecules and their easier dissociation. These results were consistent with experimental data.