The invention discloses a control method and system for a smoke exhausting draught fan of an annealing furnace. Waste gas pressure of waste gas generated by a continuous annealing furnace production line is monitored in the running process of the smoke exhausting draught fan of the annealing furnace; when the waste gas pressure is monitored to be larger than a preset pressure upper limit, a selection block is used for selecting a responding first draught fan power set value to control the smoke exhausting draught fan of the annealing furnace; and when the waste gas pressure is monitored to be smaller than a preset pressure lower limit, the selection block is used for selecting a responding second draught fan power set value to control the smoke exhausting draught fan of the annealing furnace, wherein the first draught fan power set value is larger than the second draught fan power set value. By means of the control method and system, the technical problem that in the running process of an existing smoke exhausting draught fan of an annealing furnace, triangular waveform oscillations happen to the waste gas pressure value while regular sinusoidal waveform oscillations happen to the power of the draught fan is solved effectively, the service life of the equipment is prolonged, and damage risks are lowered.