According to one embodiment of the present disclosure, a cell culture system includes: a cell culture container; a liquid storage part configured to store a liquid including a culture medium or a reagent to be supplied to the cell culture container; and a cell collection part configured to collect cells cultured in the cell culture container, wherein the cell culture container, the liquid storage part, and the cell collection part are connected by spatially closed-system lines at least during a period from feeding of the liquid to the cell culture container to removal of the cultured cells, and wherein the cell culture container is arranged in an incubator in a form of a multistage shelf including a liquid supply/discharge port.