The invention provides a hydrogenation catalyst as well as preparation and application thereof and specifically provides a petroleum fraction oil hydrogenation refining catalyst containing noble metal. The hydrogenation catalyst takes a mixture of a molecular sieve with a pore diameter less than 0.3nm, aluminum hydroxide and/or amorphous silicon-aluminum as a carrier and noble metal atoms are deposited in a molecular sieve pore channel; VIB group metal and VIII group metal are used as active metal and are loaded outside the molecular sieve pore channel, wherein by taking the total weight of the hydrogenation catalyst as 100 percent, the content of the noble metal atoms is 1 to 2 percent and the content of active metal oxide is 10 to 40 percent. The catalyst provided by the invention can sufficiently express dissociation performance of a noble metal component on hydrogen gas and enough active hydrogen atoms are provided in a reaction system, so that the catalyst has very high hydrogenation performance and aromatic hydrocarbon saturation performance; meanwhile, the catalyst has relatively high desulfurization performance through effects of a peripheral non-noble-metal component and acidic center.