To provide a temperature control method capable of equivalently maintaining qualities of substrates even when treated substrates are continuously carried in a treatment container in the case in which activation annealing treatment is performed by an electron impact heating method. The temperature control method of a substrate heat treating apparatus performing annealing treatment of a substrate by an electron impact heating method includes performing preheating for heating the inside of a treating chamber 2a at a higher temperature than the annealing treatment temperature of a substrate 21 and over a longer period of time than the annealing treatment time and then, cools the inside of the treatment container to a temperature lower than the annealing treatment temperature, prior to carrying the substrate 21 in a vacuum exhaustible container 3 and carrying the substrate 21 in the preheated vacuum exhaustible treatment container 3 and then, increasing a temperature of the treatment container to the annealing treatment temperature to perform the annealing treatment.