The invention provides an in-situ preparation method and application of a lipophilic nano molybdenum disulfide catalyst. The in-situ preparation method comprises the following steps: preparing an aqueous solution by using ammonium tetramethylammonium molybdate and a reducing agent according to a certain proportion, adding an organic solvent and a modification ligand that are insoluble in water, slowly stirring at a certain temperature to react for a certain time, and centrifuging, washing and drying the obtained product to obtain the lipophilic nano molybdenum disulfide catalyst. The prepared nano molybdenum disulfide has excellent dispersity and stability in an oil phase, is of an amorphous structure and can be decomposed into a molybdenum disulfide single piece layer in a heavy oil suspended bed hydrogenation reaction process. The amorphous nano molybdenum disulfide catalyst provided by the invention expresses extremely high catalytic hydrogenation activity and anti-coking performance in the suspended bed hydrogenation reaction of one or mixture of several of crude oil, atmospheric residue, vacuum residue, coal tar, deasphalted oil, oil sand asphalt, asphalt and coal tar asphalt.