The invention provides a preparation method of a hydrogenation catalyst. According to the method, a part of active metal components and an organic complexing agent are introduced in a carrier moldingprocess, a carrier is molded through a certain calcining treatment procedure, and then a subsequent active metal soaking step is performed to obtain the hydrogenation catalyst. According to the hydrogenation catalyst prepared with the method provided by the invention, active metals are dispersed uniformly; the preparation method is simple and feasible, and is particularly suitable for an ultra-deep hydrodesulfurization reaction of diesel oil.