A cell culture apparatus comprises at least one storage space, at least one barrier, a working space, a sterilization space, and a control space. The at least one storage space comprises a container shelf, an upright track, a rotatable holder, and a light tube. The working space comprises a filling station and an inspecting station. The filling station comprises a first delivering device, an open-close device, and a filling mechanism. The inspecting station comprises a first inspecting mechanism and a second delivering device. Also provided is a method of using the cell culture apparatus including steps of filling, inspecting, or collecting cell cultures, therefore, the cell culture apparatus performs multiple cell culture processes automatically.