A substrate depositing system comprises a substrate loading chamber for receiving a substrate, a substrate unloading chamber for withdrawing the substrate, at least one process chamber disposed between the substrate loading chamber and the substrate unloading chamber for processing the substrate, and a mask keeping chamber connected to one side of the process chamber(s). A substrate depositing method comprises inputting a substrate into a process chamber, transferring a mask to the process chamber from a mask keeping chamber connected to the process chamber, aligning the substrate and the mask, depositing a depositing material on the substrate while moving a deposition source in the process chamber, and withdrawing the substrate from the process chamber.