A water-cooling thermal dissipating system includes an electronic device and a thermal dissipating device. The electronic device includes a computing module includes a computing unit releasing heat when operation. The thermal dissipating device includes a thermal conducting unit, a pump, a tank, a thermal exchanger, and a controlling module; the thermal conductive unit is attached to the computing unit for thermal conduction; the pump is coupled to the thermal conductive unit, the pump, the tank, and the thermal exchanger for pumping a cooling-liquid therethrough, such that the cooling liquid is allowed to flow into the thermal conductive unit for absorbing heat. The controlling module generates an abnormal signal when the thermal dissipating device is sensed to be in an abnormal state, and the computing module forces to shut down the electronic device after continually receiving the abnormal signal for a predetermined time.