Flower-like intercalated MoS nanomaterials have been successfully synthesized via a microemulsion-mediated hydrothermal (MMH) method, and characterized by X-ray diffraction, Raman spectroscopy, element analysis, scanning electron microscopy, transmission electron microscopy, thermogravimetric analysis, and Fourier transform infrared spectroscopy in detail. Their catalytic performance for anthracene hydrogenation was evaluated using a slurry-bed batch reactor with an initial hydrogen pressure of 80 bar at 350 °C for 4 h. The intercalated MoS nanoflowers synthesized from Na MoO (MoS -S) and H MoO (MoS -A) as molybdenum precursors have diameters of about 150 and 50 nm, respectively. MoS nanosheets on MoS -S and MoS -A possess stacking layer numbers of 5–10 and 2–5, and slab lengths of about 15 and 10 nm, respectively. The interlayer distances of MoS -S and MoS -A are both enlarged from 0.62 nm to about 0.95 nm due to the intercalation of NH and surfactant molecules. The MoS nanoflowers have high catalytic activities for anthracene hydrogenation. The selectivity for octahydroanthracene, a deeply hydrogenated product, over MoS -A is 89.8%, which is 31.0 times higher than that over commercial bulk MoS . Fully hydrogenated product (perhydroanthracene) was also detected over MoS nanoflowers with a selectivity of 3.7%. The enhanced hydrogenation activities of MoS nanoflowers can be ascribed to the high exposure of catalytic active sites, resulting from the smaller particle size, fewer stacking layer, shorter slab length and enlarged interlayer distance of MoS nanoflowers compared with commercial bulk MoS . In addition, a possible growth mechanism of MoS nanoflowers synthesized via the MMH method was proposed.