The invention provides a brushless DC electronic water pump fault diagnosis system, which comprises an observer and a fault analysis module, wherein the observer inputs a motor angular velocity and control voltage, and a load torque observation value is obtained; the motor angular velocity is actually measured through a sensor, and the control voltage is obtained through an original brushless DC electronic water pump control system; the fault analysis module comprises a water pump operation fault analysis module; the water pump operation fault analysis module is used for comparing the load torque observation value obtained by the observer and a set load torque range, when the obtained load torque observation value is not in the load torque range, fault is judged to happen to operation of the water pump, and a plurality of load torque observation values are acquired in the case of normal water pump operation, an arithmetic mean value and a standard deviation are calculated, appropriate multiples are selected, and thus the load torque range is obtained. Detection output of the sensor is only used for data calibration, an observer model is built, and fault diagnosis is carried out on the water pump.