A method of setting an exclusive controller for a water heater, wherein a plurality of controllers are provided for user to operate to control a water heater, includes the steps of: a) Provide each controller an identification code, and saving the identification codes of the controllers in a processor of a water heater; b) Input a command through a controller, and sending the command to the processor of the water heater, wherein the command includes the identification code of the controller; c) Make a recording that the controller is an exclusive controller when the identification code in the command is identical to the identification code in the processor; d) Execute the command from the exclusive controller to control the water heater, and rejecting commands from the other controllers; and e) Repeat the step d until the recording of the exclusive controller is canceled.