In order to provide a substrate cartridge, a substrate processing apparatus, a substrate processing system, a control apparatus, and a method of manufacturing a display element capable of preventing foreign objects from being attached to the substrate, there is provided a substrate cartridge including: a cartridge mainframe that has an opening which a substrate is carried in/out and accommodates the substrate through the opening; a mount portion that is provided in the cartridge mainframe and is detachably connected to an external connecting portion; and a blocking unit that blocks the opening depending on a connection state between the mount portion and an external connecting portion.