A substrate processing system allows to reduce the number of works that should be done by a software engineer. The system 100 includes a substrate processing apparatus 101; a substrate processing controller 102 for controlling the substrate processing apparatus 101; and a server 103 for storing therein commands, i.e., instructional statements, for defining an operation of each device. The substrate processing controller 102 has a RAM 105 serving as a work space for creating a macro file corresponding to each of processes divided from the whole substrate processing or for changing the content of a macro file; and an executor 108 composed of, e.g., CPU for executing a process sequence macro obtained by a combination of the created macro files. The user creates a macro file describing a sequential operation of each process or changes the content of a macro file by arranging the stored commands.