An apparatus for controlling a heat dissipation value of a fuel cell having a plurality of fuel cell stacks (210, 220, 230 and 240), mechanically connected to each other, the fuel cell stacks receiving fuel and air, the apparatus comprising: a plurality of stack condition sensors (310, 320, 330 and 340) sensing temperature, current and voltage of the fuel cell stacks (210, 220, 230 and 240), and a switching unit (100 and 400) electrically connecting the fuel cell stacks (210, 220, 230 and 240), and heating value conditioning unit (510 and 520) controlling heat dissipation value of the fuel cell stacks (210,220,230 and 240) and control unit controlling the heating value conditioning unit (510 and 520) based on sensing signal of the stack condition sensors (310, 320, 330 and 340), characterized in that the control unit calculates heat dissipation value of the fuel cell stacks (210, 220, 230 and 240) based on the sensing signal of the stack condition sensors (310, 320, 330 and 340); in case that the heat dissipation value deviates a preset heat dissipation value threshold range, controls the switching unit (100 and 400) to form a plurality of conditioning target stack group consisting of the fuel cell stacks that the heat dissipation value deviates the threshold range; and generates control signal for controlling the heating value conditioning unit (510, 520) to minimize a heat dissipation value difference of the fuel cell stacks (210, 220, 230 and 240) that the heat dissipation value deviates the threshold range, the heating value conditioning unit (510, 520) conditions the heat dissipation values of conditioning target stack group to be maintained within the threshold range, based on the control signal transmitted from the control unit, or the heat dissipation value is calculated by a following equation: P = I × Δ ⁢ V, wherein P is the heat dissipation value, I is a present operating current, and ΔV is a voltage loss being a voltage difference between an open circuit voltage and a present voltage of stack. a plurality of stack condition sensors (310, 320, 330 and 340) sensing temperature, current and voltage of the fuel cell stacks (210, 220, 230 and 240), and a switching unit (100 and 400) electrically connecting the fuel cell stacks (210, 220, 230 and 240), and heating value conditioning unit (510 and 520) controlling heat dissipation value of the fuel cell stacks (210,220,230 and 240) and control unit controlling the heating value conditioning unit (510 and 520) based on sensing signal of the stack condition sensors (310, 320, 330 and 340), characterized in that the control unit calculates heat dissipation value of the fuel cell stacks (210, 220, 230 and 240) based on the sensing signal of the stack condition sensors (310, 320, 330 and 340); in case that the heat dissipation value deviates a preset heat dissipation value threshold range, controls the switching unit (100 and 400) to form a plurality of conditioning target stack group consisting of the fuel cell stacks that the heat dissipation value deviates the threshold range; and generates control signal for controlling the heating value conditioning unit (510, 520) to minimize a heat dissipation value difference of the fuel cell stacks (210, 220, 230 and 240) that the heat dissipation value deviates the threshold range, the heating value conditioning unit (510, 520) conditions the heat dissipation values of conditioning target stack group to be maintained within the threshold range, based on the control signal transmitted from the control unit, or the heat dissipation value is calculated by a following equation: P = I × Δ ⁢ V, wherein P is the heat dissipation value, I is a present operating current, and ΔV is a voltage loss being a voltage difference between an open circuit voltage and a present voltage of stack. characterized in that the control unit calculates heat dissipation value of the fuel cell stacks (210, 220, 230 and 240) based on the sensing signal of the stack condition sensors (310, 320, 330 and 340); in case that the heat dissipation value deviates a preset heat dissipation value threshold range, controls the switching unit (100 and 400) to form a plurality of conditioning target stack group consisting of the fuel cell stacks that the heat dissipation value deviates the threshold range; and generates control signal for controlling the heating value conditioning unit (510, 520) to minimize a heat dissipation value difference of the fuel cell stacks (210, 220, 230 and 240) that the heat dissipation value deviates the threshold range, the heating value conditioning unit (510, 520) conditions the heat dissipation values of conditioning target stack group to be maintained within the threshold range, based on the control signal transmitted from the control unit, or the heat dissipation value is calculated by a following equation: P = I × Δ ⁢ V, wherein P is the heat dissipation value, I is a present operating current, and ΔV is a voltage loss being a voltage difference between an open circuit voltage and a present voltage of stack.