The invention discloses an ecological seawater rare fish factorization circulating water aquaculture system which comprises an aquaculture pond, a primary filter tower, an albumen segregator, a primary biological filter tower, a secondary biological filter tower, a tertiary biological filter tower, an algae treating pond, a source water filter pond, a UV (Ultraviolet) sterilizer, a temperature adjusting pond, an arc-shaped sieve, a primary sedimentation pond and a secondary sedimentation pond. A bidirectional drainage system is adopted by the aquaculture pond, the water containing less smaller particles at the lower part of the pond and the water containing more larger particles at the bottom of the pond are respectively drained and then input into different processing units for recycle. Molluscs, sea cucumbers and algae are drawn into aquaculture waste, wastewater disposal and resource utilization by the circulating water aquaculture system, so that the circulating water aquaculture system has an obvious ecological characteristic. The ecological seawater rare fish factorization circulating water aquaculture system has the advantages of high treatment efficiency of aquaculture wastewater and rubbish, simpler equipment, low energy consumption, high backwash efficiency, resource utilization of aquaculture wastewater and rubbish, less circulation supplement water, high treatment efficiency of inorganic nutrient salt in the water and high economic additional value.