The invention discloses a method for hydrogenation catalyst containing molecular sieve and amorphous silicon aluminum. The method includes: adding a mixture of molecular sieves containing hydrogenation active metal components and organic amines, organic alcohols and / or organic acids during the gelation of amorphous silica-alumina, and aging after the gelation of amorphous silica-alumina is completed. , followed by hydrothermal treatment, filtration, washing, drying, molding, drying and roasting to obtain a hydrogenation catalyst. The method of the invention can organically combine the molecular sieve and the amorphous silica-alumina, has a good degree of combination and dispersion, can avoid agglomeration or even blockage between the molecular sieve and the amorphous silica-alumina, and can effectively adjust the hydrogenation function of the catalyst With cracking function, improve the performance of the catalyst. The catalyst prepared by the method of the invention is suitable for shallow cracking and deep hydrogenation processes.