The invention discloses a control method for heat treatment of an amorphous alloy three-dimensional wound iron core. The control method comprises the following steps of inserting a plurality of thermocouples into intersection points between the centers of the stack thicknesses and the centers of the widths of a plurality of single iron cores in a one-to-one correspondence manner; placing a three-dimensional wound iron core into an annealing furnace and opening all heating devices in all subareas in the annealing furnace for starting heating; in the heating process, monitoring the real-time temperature of one single iron core corresponding to each thermocouple by each thermocouple; when each thermocouple monitors that the real-time temperature of the corresponding single iron core reaches a set value, adjusting the power of the heating device in the subarea closest to the single iron core or closing the heating device in the corresponding subarea and stopping heating; when the thermocouples monitor that the temperatures of all the single iron cores reach the set values, starting timing and heat preservation; after the heat preservation is finished, closing the heating devices in all the subareas in the annealing furnace, and starting cooling until the temperature of each iron core is reduced to room temperature. According to the control method for heat treatment, disclosed by the invention, the uniformity of the amorphous alloy three-dimensional wound iron core can be guaranteed.