The invention discloses an electric heating overtemperature protection apparatus for an air conditioner of a motor train and a protection method for the protection apparatus. The lower ends of a first-level temperature control protection switch and a flow switch are connected with the power supply common end of a controller after being connected in parallel; the upper ends of the first-level temperature control protection switch and the flow switch are connected with the signal acquisition input end of the controller; and a second-level temperature control protection switch is serially connected into a main loop of an electric heater. According to the electric heating overtemperature protection apparatus and the protection method, a reason for overtemperature of the electric heater is analyzed and an overtemperature phenomenon of the electric heater is prevented by creatively applying the flow switch, so that the service life of the electric heater is prolonged and the fault rate of the electric heater is reduced; and the influence of external interference on operation of the electric heater is reduced in a multilevel fault handling mode, the possibility of frequent start and stop of the electric heater is avoided, and the service life of the electric heater, cables and contactors is prolonged.