To prevent unevenness in thermal history of each substrate due to substrate supply failure without causing the increase of the cost and the device size.

A substrate thermal treatment system 10 of this invention includes a thermal treatment device 1, a carry-in conveyor 2, a carry-out conveyor 3, a first rack 4, a transfer robot 6, and a control part 7. The thermal treatment device 1 includes multiple substrate housing parts 11 therein. The transfer robot 6 carries in substrates 100 sequentially from a receiving position 22 to each substrate housing part 11, carries out the substrates 100 sequentially from each substrate housing part 11 to a take out position 32, and carries in shield plates 200 from the first rack 4 to the substrate housing parts 11. The control part 7 controls the operation of the transfer robot 6 so that the transfer robot 6 carries in the shield plate 200 instead of the substrate 100 when the transfer robot 6 does not receive the substrate 100 during the substrate carry-in operation.