A blower unit of an air conditioner for a vehicle which allows one actuator to drive two doors in a structure in which at least two doors are provided in an intake duct is disclosed. The blower unit of an air conditioner for a vehicle includes an intake duct including an internal air inlet through which internal air is introduced and an external air inlet through which external air is introduced, a first door configured to adjust an opening amount of a part of the external air inlet and an opening amount of the internal air inlet, and a second door configured to adjust an opening amount of the remaining part of the external air inlet, wherein the first door and the second door are linked and driven together.