Provided are a system and method of controlling an in-vehicle device using augmented reality. A system for controlling an in-vehicle device using augmented reality includes a mobile device configured to identify a vehicle object unit as an image and receive a vehicle control command through implementation of the augmented reality of the image, and a driving control unit configured to transmit a vehicle type information to the mobile device and, upon receiving a command signal from the mobile device, to control the in-vehicle device that corresponds to the command signal. Accordingly, by remotely controlling an in-vehicle device by using augmented reality of a mobile device, user convenience may be improved.