The present invention relates to a blower unit of an air conditioner for a vehicle, which can effectively prevent water from being introduced into a motor and has a motor housing and a blower wheel improved to smoothly perform cooling of the motor. The blower unit of a two-layered air conditioner for a vehicle, which can divide and inhale indoor air and outdoor air, includes: a scroll case having an upper passageway and a lower passageway; a first blower wheel disposed in the upper passageway; a second blower wheel disposed in the lower passageway and arranged below the first blower wheel; a blower motor for rotating the first blower wheel and the second blower wheel; and a motor housing for covering the blower motor, wherein a hub for guiding air is disposed on the second blower wheel, and the hub of the second blower wheel is partially overlapped with an end portion of the motor housing.