The invention discloses a fixed bed hydrogenation reactor and an application method thereof. In the fixed bed hydrogenation reactor, a gas-liquid phase product pre-separation technology with gas phase withdrawal in an axial center position is employed, wherein a plurality layers of baffle plates are arranged on the inner wall of the reactor, thereby improving operation stability of the hydrogenation system, improving gas-liquid distribution status in the reactor and eliminating wall flow, deflected flow and the like defects. The reactor, when being used in a reaction process of C3 fraction liquid-phase selective hydrogenation to remove methyl acetylene (MA) and propadiene (PD), can not only increase the MAPD hydrogenation purification reaction efficiency of a propadiene material but also is low in residual hydrogen, so that separation load in a down-stream propylene rectification column is reduced.