Recirculating aquaculture system (RAS), as a modern highly intensive aquaculture mode, demonstrates the advantages of environmental friendliness, high efficiency and sustainable development, and has been widely used worldwide; they are also expected to be more widely applied in industrial aquaculture in the future as our natural resources are decreasing. However, RAS imposes very high requirements on operating conditions, including temperature, salinity, dissolved oxygen, pH, stocking density, light, feed composition, feeding amount, feeding frequency, and disinfection methods. Each factor is critical to the stable operation of the system. Therefore, to ensure the efficient and stable operation of RAS, its influencing factors must be controlled to within appropriate ranges. Herein, the factors affecting the operation of RAS are reviewed, and the mechanisms of their influence on the reared organisms are revealed, and suggestions on the control of these factors in aquaculture are proposed. This review can provide a theoretical basis for the further development of RAS.