Abstract: The present disclosure provides a fully enclosed cell culture system, including at least an incubator, a bioreactor, a gas flow assembly, a liquid flow assembly, a temperature adjustment assembly, and a central controller. The system realizes a thermostatic incubation environment. Cells are incubated by perfusion, and a fully enclosed integrated process from cell activation, infection and amplification to finished product harvesting is achieved. By axially stirring the cells and an incubation liquid in a tank body, a radial shear force is reduced, which effectively protects the cells and improves the cell yield. In the system of the present disclosure, gases are separately introduced, ensuring that the content of each gas component is stable in the incubation process. The cell incubation is not directly affected by changes of outside gases in the cell incubation process, which improves culture efficiency.