There is provided a substrate cleaning system which is capable of cleaning wafers W in a high cleanliness atmosphere with high accuracy taking an advantage of a sheet-type wet cleaning treatment, and which is simple and compact in construction, and is excellent in cost performance. The system comprises a system body 1 capable of being sealed, a loading/unloading booth A comprising a substrate carry-in section Aa in which a plurality of substrates are stocked and standby to be carried in before cleaning treatment is applied to them and a substrate carry-out section Ab in which a plurality of substrates are stocked and standby to be carried out after cleaning treatment is applied to them, a processing booth C provided with at least one sheet-type substrate cleaning chamber 10 in the cleaning treatment can be applied to a plurality of substrates by a plurality of cleaning solutions, and a robot booth B provided with a transport robot for transporting the substrates one by one between the processing booth C and the loading/unloading booth A, wherein the respective booths are partitioned by partition walls each having a required minimum cross sectional area.