An electronic system comprising an electronic device and an indicating device is provided. The indicating device includes a wireless communication circuit configured to be communicated with the electronic device, a switch circuit, a motion sensor for detecting a movement of the indicating device, and a control unit coupled to the wireless communication circuit, the motion sensor and the switch circuit. In a period that the switch circuit is triggered, the motion sensor detects a plurality of three-dimensional rotation matrices of the indicating device in the space. A movement trace of the indicating device is computed by the electronic device according to the three-dimensional rotation matrices, and a corresponding operating function is enabled according to the movement trace. An operating method and an indicating device is further provided.