There is disclosed a substrate processing method by a multi-patterning technique, which comprises a lithography process and an etching process, each of the processes is performed to one substrate at least twice. The substrate processing method is performed by using a substrate processing system comprising a plurality of process units for performing respective steps of the lithography process. When a second lithography process is performed to a substrate, process unit(s) for performing one or more steps of the second lithography process to be used in the second lithography process is automatically selected based on the process history of the first lithography process in such a way that the process unit(s) to be used in the second lithography process is (are) identical to the processed unit(s) used in the first lithography process.