The invention discloses a beneficiation process of lean magnetite ores and a production system thereof, and belongs to the technical field of beneficiation. The beneficiation process comprises the following steps: coarse crushing, intermediate crushing, magnetic separation and transferring. An intermediate crushing device is placed at the front of an ore stope, coarse crushing, intermediate crushing and dry magnetic separation are directly carried out on the stope, the purpose of 'early throwing and discarding' tailings and waste rock is achieved, the grade of rough concentrates is improved, the conveyance amount of the ores is reduced, the conveyance cost of the ores is also reduced, the service lives of a belt and a funnel lining plate of a magnetic separator are prolonged, and therefore, the operation cost of a mine is reduced effectively. The production system comprises a coarse crusher, a screening machine, an intermediate crusher, the magnetic separator, a belt conveyor I and a belt conveyor II, wherein the coarse crusher, the screening machine, the intermediate crusher and the magnetic separator are successively arrayed according to a production line in the ore stope; the belt conveyor I conveys the tailings and the waste rock to a dumping site after the tailings and the waste rock are separated magnetically; and the belt conveyor II conveys magnetically separated rough concentrates to a follow-up process. An iron ore extraction region is expanded, and for the actual situation that lean iron ores are main iron ores in China, the beneficiation process of the lean magnetite ores and the production system thereof are particularly worthy of being popularized and used.