A wafer transfer system for use in a photolithography system including a wafer storage apparatus, a pre-alignment apparatus, a buffer stage and a wafer stage is disclosed, which includes: a dual-arm robot, configured to take a wafer to be exposed from the wafer storage apparatus and transfer it onto the pre-alignment apparatus and further configured to remove an exposed wafer from the buffer stage and place it back into the wafer storage apparatus; a wafer-loading linear robot, configured to transfer a pre-aligned wafer onto the wafer stage; and a wafer-unloading linear robot, configured to transfer the exposed wafer onto the buffer stage. The dual-arm robot, the wafer-loading linear robot and the wafer-unloading linear robot can operate in parallel so as to achieve time savings in the wafer transfers.