The invention relates to a surface-amphiphilic nanometer composite sulfide hydrogenation catalyst, a preparing method thereof and applications of the catalyst. A nickel source and/or a cobalt source and/or an iron source, a sulfur-containing molybdenum source and/or a sulfur-containing tungsten source, a sulfur source, an ionic liquid, a reductant and deionized water are prepared into an initial reaction mixture, the initial reaction mixture is crystallized in a sealed autoclave under hydro-thermal conditions, and the catalyst is obtained after product separation. The ionic liquid is used in the synthetic system, and the prepared sulfide has a nanometer size and surface amphipathicity, and has extremely good dispersibility and catalytic activity in polar and nonpolar catalytic systems. The catalyst shows extremely good catalytic activity in suspended-bed hydrogenation deasphalting, hydrodesulfurization, hydro-denitrification, aromatic hydrocarbon hydrogenation, and the like of coal tar, heavy oil, extra-heavy oil, residue oil, shale oil, and other types of heavy oil, and has a good application prospect in photovoltaic conversion, water photocatalysis to produce hydrogen, and other reactions.