The invention provides a micro-interface enhanced reaction system and method for petroleum resin hydrogenation. The micro-interface enhanced reaction system comprises a pre-hydrogenation reactor provided with two catalyst bed layers, a circulating hydrogen channel and a new hydrogen channel, a built-in micro-interface generator is arranged between the two catalyst bed layers, and an external micro-interface generator is arranged on the side surface of the pre-hydrogenation reactor. After the micro-interface enhanced reaction system provided by the invention is combined with the micro-interfacegenerator, the energy consumption is reduced, the reaction temperature is reduced, the reaction yield is improved, the utilization rate of raw materials is improved, particularly the utilization rateof hydrogen is improved, and meanwhile, the productivity is effectively improved.