The invention discloses a control system and a control method for an electric heater of a plateau train. The system comprises a central processor, a data storage module, a temperature detection module, a pressure detection module, a display module and an electric heater control module respectively connected with the central processor. Wherein, a temperature detection module is used for detecting the temperature inside and outside the vehicle compartment and the surface temperature of the electric heater cover; A pressure detection module, configured to detect the air pressure inside and outside the train compartment; The central processing module is used for calculating the heat load of the train in heating season, calculating the heat dissipation amount of the electric heater, and preliminary calculating and checking the number of the radiators according to the data detected by the temperature detecting module and the pressure detecting module. An electric heater control module, configured to control the opening number of the electric heater and the surface temperature of the electric heater cover. The invention has the beneficial effects of ensuring that the temperature in the train meets the requirements of the specifications and ensuring that the surface temperature of the electric heater cover is not higher than the safety temperature.