A burner control system for controlling loads such as a blower motor and an electronic pump of a burner which comprises a drive voltage regulating circuit for varying the drive voltages corresponding to the loads to thereby vary the amount of heat being generated from the burner in the actuated condition. A microprocessor outputs a plurality of load control signals. A drive signal generating circuit for initiating in response to the plurality of load control signals received from the microprocessor generates a plurality of drive signals for driving the loads. A driving circuit powers the loads in accordance with the plurality of drive signals from the drive signal generating circuit. A method for controlling loads such as a blower motor and an electronic pump of a burner comprises the steps of selecting drive voltages corresponding to the loads, selecting data corresponding to the selected drive voltages to output a plurality of load control signals; and receiving the plurality of load control signals to power the loads. Therefore, the thermal efficiency of the burner can be increased by preventing incomplete combustion which results from the unbalanced output of the blower motor with the amount of fuel being supplied by the electronic pump.