A substrate processing system 1 comprises a first detecting part 40 configured to detect unprocessed wafers W, and a second detecting part 50 configured to detect processed wafers W. The first detecting part 40 is configured to detect whether the unprocessed wafers W are respectively accommodated in respective accommodating portions 82 of a container 80 or not, and to detect accommodated conditions of the respective unprocessed wafers W accommodated in the respective accommodating portions 82. The second detecting part 50 is configured to collectively detect whether the processed wafers W are respectively accommodated in the respective accommodating portions 82 of the container 80.