The invention discloses a fish-bacterium-algae-symbiotic ecological breeding system and a running method thereof. The fish-bacterium-algae-symbiotic ecological breeding system and the running method mainly aim at reducing aerating cost, improving the use efficiency of nitrogen and organisms and improving purification of breeding waste water. The system is composed of a fishpond, a photobioreactor, a membrane assembly, a light source and an aerating system, and is characterized in that aquaculture is combined with a bacterium-algae-symbiotic system and the membrane technology, the photosynthesis of microalgae continues, the dissolved oxygen concentration of processed waste water is high, healthy breeding of fishes is guaranteed, and aerating cost is reduced; due to excellent organism degradation and absorption of bacteria, the organism recycling capacity of the system is improved; due to the comprehensive synergistic effect of microalgae and microorganisms, waste water processing efficiency is improved; as microalgae absorb nitrogen substances, the nitrogen use efficiency of the system is improved; in addition, due to the adoption of the membrane technology, microalgae can be more easily harvested.