The invention discloses a method and a system for processing a remote controller connection. The method comprises the steps of connecting a remote controller and a remotely controlled device via a Bluetooth, and after the Bluetooth pairing is successful, monitoring whether the remote controller has an operation; when the remote controller has no operation and the remotely controlled device is in a starting-up state, keeping the remote controller in a shallow dormancy mode connection all the time, namely controlling the Bluetooth of the remote controller to keep a scanning state, sending a data packet once every a first preset time, controlling and monitoring an energy of the remote controller in a Bluetooth state to be in the first energy; and when monitoring the Bluetooth connection between the remote controller and the remotely controlled device is disconnected, controlling the remote controller to start a dormancy mode, wherein the Bluetooth is closed when in the dormancy mode, the energy is controlled in the third energy, and a working mode can be awakened via any key. According to the method and the system disclosed by the invention, on the basis of the prior art, the energy mode of the remote controlled is modified, so the experience problem possibly due to a reconnection speed is solved, and the energy is guaranteed to be at a relatively low level.