Abstract: A substrate manufacturing system comprises a substrate processing device for conveying pallets from an inlet to an outlet; a pallet conveyor for sequentially returning the pallets for conveying the pallets from an outlet to an inlet; and a pallet controller including: a counter for counting the conveyed pallets at the inlet of the substrate processing device, a reference detector for detecting the reference pallet at the inlet of the substrate processing device, a first monitor for activating first alarm when the substrate lot is changed at the inlet of the substrate processing device and the reference detector detects absence of the reference pallet at the inlet of the substrate processing device, and a second monitor for activating second alarm when the counter counts the predetermined number of the pallets and the reference detector detects absence of the reference pallet at the inlet of the substrate processing device.