A system for controlling a relay using a flip-flop in a Battery Management System, the system comprising: a control unit generating an input signal for outputting a relay control signal; a clock signal generating unit transmitting and receiving a communication signal to and from the control unit and generating a clock signal for outputting the relay control signal; a flip-flop receiving the clock signal and the input signal and outputting the relay control signal based on the received clock signal and input signal; and a relay receiving the relay control signal and transiting an operation state based on the received relay control signal, an isolator positioned over a boundary between the high-voltage region and the low-voltage region of the BMS transferring the input signal from the control unit to the flip-flop and preventing power collision between the high-voltage region and the low-voltage region; a transformer positioned over a boundary between the high-voltage region and the low-voltage region of the BMS and transferring the communication signal generated by the clock signal generating unit and transferred from the high-voltage region side to the low-voltage region and transferring the communication signal generated by the control unit and transferred from the low-voltage region side to the high-voltage region; and a signal converting unit positioned on a communication connection path of the control unit and the clock signal generating unit and converting the communication signal so as to be detected by both the control unit and the clock signal generating unit, wherein the clock signal generating unit is positioned in the high-voltage region in the BMS, operated by receiving battery power of a vehicle, and supplies power to the flip-flop. a control unit generating an input signal for outputting a relay control signal; a clock signal generating unit transmitting and receiving a communication signal to and from the control unit and generating a clock signal for outputting the relay control signal; a flip-flop receiving the clock signal and the input signal and outputting the relay control signal based on the received clock signal and input signal; and a relay receiving the relay control signal and transiting an operation state based on the received relay control signal, an isolator positioned over a boundary between the high-voltage region and the low-voltage region of the BMS transferring the input signal from the control unit to the flip-flop and preventing power collision between the high-voltage region and the low-voltage region; a transformer positioned over a boundary between the high-voltage region and the low-voltage region of the BMS and transferring the communication signal generated by the clock signal generating unit and transferred from the high-voltage region side to the low-voltage region and transferring the communication signal generated by the control unit and transferred from the low-voltage region side to the high-voltage region; and a signal converting unit positioned on a communication connection path of the control unit and the clock signal generating unit and converting the communication signal so as to be detected by both the control unit and the clock signal generating unit, wherein the clock signal generating unit is positioned in the high-voltage region in the BMS, operated by receiving battery power of a vehicle, and supplies power to the flip-flop.