Disclosed is a multi-fuel cell system and control method thereof in which when a plurality of fuel cell units electrically connected to each other, each including a fuel cell, an air compressor, and a humidifier, is cold-started, a first fuel cell unit, one of the plurality of fuel cell units, generates power in a defrost mode, an air compressor of a second fuel cell unit, another fuel cell unit, is driven by providing the power generated by the first fuel cell unit to the second fuel cell unit, and the first fuel cell unit generates power in a heating mode and the second fuel cell unit generates power in the defrost mode when the defrosting of the first fuel cell unit is completed.