The invention provides a control method and system of a draught fan and an air conditioning system. The control method of the draught fan is used for controlling a rotating speed of the draught fan inthe air conditioning system, and the air conditioning system is provided with a plurality of draught fans. The control method of the draught fan comprises the following steps that a target rotating speed St of the draught fan is obtained; whether faults exist in parts of the multiple draught fans or not is detected; when the faults exist in parts of the multiple draught fans, initial setting rotating speed limit values S1 of the draught fans without the faults in the multiple draught fans are obtained; when S1<100%, the initial setting rotating speed limit values S1 of the draught fans without the faults are adjusted to obtain compensation setting rotating speed limit values S2, and the S2=S1+XS1/(N-X). According to the scheme provided by the control method and system of the draught fan and the air conditioning system, rotating speed margins of the draught fans without the faults can be used fully, the performance of the draught fans is used fully, and when partial faults of the draught fan in the air conditioning system occur, rotating speed losses of a fault draught fan can be ensured to be compensated by using a mode of increasing the rotating speed of the draught fans withoutthe faults, a refrigeration capacity of the air conditioning system is enabled to be corrected appropriately, and the refrigeration capacity of the air conditioning system is ensured.