The invention relates to a factory circulating water fish culture system and a using method thereof, relating to the technical field of aquaculture. The factory circulating water fish culture system comprises a fishpond (1), a sedimentation interception pond (2), a biological moving bed (3), a reticular filter material filtering pond (4), a regulation pond (5) and a backwater oxygenation pipe (6), wherein the fishpond (1) is in a rectangular shape, water inside each unit can rotationally flow in one direction, and the rotational directions of adjacent units are inverse; the front half part of the sedimentation interception pond (2) is provided with a multi-bucket sewage collecting tank and a drainage through pipe, and the rear half part of the sedimentation interception pond (2) is provided with three-dimensional elastic packing; the biological moving bed (3) is formed by in series connecting a front group with a rear group, the lower part of a middle partition wall is provided with a plurality of large through hole structures, the middle of each group is provided with a partition plate (3b), suspended filter materials (3a) are placed in a cavity, and an aeration through pipe (3c) is horizontally arranged; the reticular filter material filtering pond (4) and the regulation pond (5) are connected in parallel, the lower part of the reticular filter material filtering ponds (4) and the lower part of the regulation pond (5) are communicated, reticular filter materials are taken, and a filter screen covers on the reticular filter materials; and the regulation pond (5) is used for replenishing the water, regulating pH concentration and increasing temperature and is provided with an air stripping pipe. The invention has low investment, high efficiency, energy and electricity saving and low operating cost and promotes the development of a factory circulating water fish culture career in China.