The invention discloses a reaction system for carrying out hydrodechlorination upon chlorine-containing diesel, and provides a method for carrying out hydrodechlorination upon chlorine-containing diesel with the system. According to the invention, chlorine-containing diesel and hydrogen are sequentially introduced into a hydrogenation reactor and a dechlorination tank which are connected in series, and are subjected to contact reactions with a hydrofining catalyst bed layer of the hydrogenation reactor and a hydrodemetallization agent bed layer and dechlorination agent bed layers of the dechlorination tank; according to the flow direction of the chlorine-containing diesel and hydrogen, the hydrofining catalyst is packed in the hydrogenation reactor; the hydrodemetallization agent, a dechlorination agent I and a dechlorination agent II are sequentially packed in the dechlorination tank. According to the method, the chlorine-containing diesel produces ammonium chloride in the hydrogenation reactor; with a method of graded packing of the hydrodemetallization agent and the dechlorination agents in the dechlorination tank, iron-containing impurities and ammonium chloride from the hydrogenation reactor are removed. Compared with existing technologies, the method has two advantages: first, the iron-containing impurities are uniformly deposited in the hydrodemetallization agent, such that long-period operation of the dechlorination agents is maintained; second, the graded packing of the two dechlorination agents assists in improving the utilization rates of the dechlorination agents, such that the lives of the dechlorination agents are prolonged, and the costs of the dechlorination agents are reduced.