Disclosed is a wafer conveying system for a clean room which is high in wafer conveying efficiency, and makes it possible to achieve a variety of processing operations with high efficiency. The wafer conveying system in a clean room comprises: an interface equipment cooperating with a conveying system to transfer wafers therebetween which is adapted to convey articles between manufacturing lines; a conveying path extended from the interface equipment; on intra-bay wafer conveying equipment which is moved along the conveying path; and a single or plural wafer processing equipments arranged along the conveying path, thus forming one processing line, the conveying system operating to convey cassettes containing wafers, the interface equipment operating to take a specified number of wafers out of a single or plural cassettes which are delivered to the interface equipment, and place the wafers in an auxiliary cassette provided for the one processing line only, and the intra-bay wafer conveying equipment operating to receive the auxiliary cassette, and move to a specified one of the wafer processing equipments, and to give the wafers to the specified wafer processing equipment and receive wafers therefrom.