The invention provides a heavy oil hydrogenation catalyst and a preparation method thereof. The preparation method comprises the following steps: introducing a phosphorus source in the preparation process of a Y molecular sieve to obtain a phosphorus-containing NaY molecular sieve; converting the phosphorus-containing NaY molecular sieve into a phosphorus-containing hydrogen-type Y molecular sieve; preparing a solution from a titanium precursor and an aluminum precursor; adding the phosphorus-containing hydrogen-type Y molecular sieve, and hydrolyzing the solution to obtain a micro-pore/meso-pore oxide composite carrier; adding cobalt salt or nickel salt into the solution for preparing the micro-pore/meso-pore oxide composite carrier, and hydrolyzing the solution to obtain a metal-modified micro-pore/meso-pore oxide composite carrier; dropwise adding a solution of active components of nickel-tungsten or nickel-molybdenum into the metal-modified micro-pore/meso-pore oxide composite carrier; and immersing, drying and roasting to obtain the heavy oil hydrogenation catalyst. The catalyst provided by the invention can meet requirements on diffusion, hydrogenolysis and hydrogenation reaction of heavy oil macro-molecules, and is excellent in hydrogenation-denitrification activity on heavy oil.