A bi-power motor controlling system includes a motor, a system apparatus and a motor controlling apparatus. The system apparatus has a rotational-speed target value for determining the targeted rotational speed of the motor. In addition, the system apparatus outputs a first power and a second power to the motor and the motor controlling apparatus, respectively. The motor controlling apparatus detects the motor to obtain a first rotational-speed value of the motor, and then adjusts the rotational speed of the motor to a second rotational-speed value according to the first rotational-speed value. Then, the motor controlling apparatus further generates a rotational-speed feedback signal to the system apparatus. The system apparatus adjusts the outputted first power in accordance with the rotational-speed feedback signal to make the rotational speed of the motor reach the rotational-speed target value.