The invention provides a factorized circulating water high-density three-dimensional ecological breeding system which comprises a plurality of breeding tanks, a breeding circulating water treating system communicated with the breeding tanks, and three-dimensional spraying aquaculture columns arranged on the upper portions of the breeding tanks. The factorized circulating water high-density three-dimensional ecological breeding system is characterized in that the breeding circulating water treating system comprises a water collection tank, a water pump, a microfilter, a decarburization area, a nitration area, a degassing area, an ultraviolet sterilizing area and a temperature adjusting and tempering tank sequentially along a water flow direction, the water collection tank is communicated with the breeding tanks through sewage inlets, and the temperature adjusting and tempering tank is communicated with the three-dimensional spraying aquaculture columns through a clean water outlet and the water pump; a biological filtering area or a low-speed nitration area are arranged between the nitration area and the degassing area; a mud blocking slot is formed between the decarburization area and the nitration area, a plurality of mud-blocking water-passing holes are formed in a wall of the decarburization area on one side of the mud blocking slot, a plurality of nitration water incoming holes are formed in a wall of the nitration area on the other side of the mud blocking slot, and bottom height of the mud-blocking water-passing holes is greater than height of a mud discharging pipe in the decarburization area. The factorized circulating water high-density three-dimensional ecological breeding system is low in investment, high in space utilization rate, healthy and efficient.