A method and system for controlling an Audio Video Navigation (AVN) of a vehicle by a smart device are disclosed, which control the AVN by a smart device including a mobile phone carried by a passenger accommodated on a back seat of the vehicle, using beacon and physical web technologies, controlling various functions of the AVN embedded in the vehicle may include constructing a virtual tunnel connected to an Internet of Things (IoT) server, acquiring an external Uniform Resource Locator (URL) for a service from the IoT server, generating the acquired external URL as a beacon packet, and transmitting the generated beacon packet to the smart device using a Bluetooth Low Energy (BLE) signal within the vehicle.