A fuel cell system comprising: a first converter, a fuel cell stack and a battery, the first converter being connected to the fuel cell stack and the battery and being configured to convert power, which is output from the fuel cell stack or the battery, into power in a specific level; a second converter configured to convert power which is input to or output from the battery; a super capacitor; a power relay assembly configured to control power flow between the super capacitor and the first converter; and a controller configured to control outputs of the first converter and the second converter, depending on a starting state or an operating state of the fuel cell system, and to control an operation of the power relay assembly, wherein the first converter is disposed on a main bus stage to connect the fuel cell stack to an inverter, and wherein the second converter has one end connected to the main bus stage between the fuel cell stack and the first converter, and an opposite end connected to the battery, and is configured to adjust bi-directional power flow; wherein the power relay assembly has one end connected to the main bus stage between the first converter and the inverter, and an opposite end connected to the super capacitor, and is configured to adjust bi-directional power flow; wherein the second converter is configured to supply starting power of the fuel cell system and charging power of the super capacitor, by using power discharged from the battery, when the fuel cell system is started, and wherein the first converter is configured to supply the charging power, which is received from the second converter, to the super capacitor through the power relay assembly, when the fuel cell system is started. a first converter, a fuel cell stack and a battery, the first converter being connected to the fuel cell stack and the battery and being configured to convert power, which is output from the fuel cell stack or the battery, into power in a specific level; a second converter configured to convert power which is input to or output from the battery; a super capacitor; a power relay assembly configured to control power flow between the super capacitor and the first converter; and a controller configured to control outputs of the first converter and the second converter, depending on a starting state or an operating state of the fuel cell system, and to control an operation of the power relay assembly, wherein the first converter is disposed on a main bus stage to connect the fuel cell stack to an inverter, and wherein the second converter has one end connected to the main bus stage between the fuel cell stack and the first converter, and an opposite end connected to the battery, and is configured to adjust bi-directional power flow; wherein the power relay assembly has one end connected to the main bus stage between the first converter and the inverter, and an opposite end connected to the super capacitor, and is configured to adjust bi-directional power flow; wherein the second converter is configured to supply starting power of the fuel cell system and charging power of the super capacitor, by using power discharged from the battery, when the fuel cell system is started, and wherein the first converter is configured to supply the charging power, which is received from the second converter, to the super capacitor through the power relay assembly, when the fuel cell system is started.