A method for controlling an intake of an air-conditioner of a vehicle is disclosed. The method includes the a-1) step (S1) at which the main door (220) of the intake (200) opens the outdoor-air inlet port (211) and closes the indoor-air inlet port (212), so that only outdoor air flows into the intake, the b-1) step (S2) of detecting operation of the blower (130), the c-1) step (S3) of determining whether set indoor temperature of the vehicle is predetermined temperature or higher, and the d-1) step (S4) at which the subsidiary door (230) opens the subsidiary indoor-air inlet port (213) so that some indoor air flows into the intake. The method automatically controls the intake of the air-conditioner, thus allowing some indoor air to flow into the intake while outdoor air is flowing into the intake, therefore keeping the indoor temperature of the vehicle pleasant, and enhancing heating efficiency.