A power distribution method and system for a fuel cell vehicle is provided. The method includes deducing an amount of moisture in a stack of a fuel cell, when a supply amount of air of the stack of the fuel cell is decreased and determining a state of the fuel cell based on the amount of moisture. Additionally, the method includes deducing allowance power of a regenerative braking of a driving motor using maximum power of the regenerative braking of an air compressor and chargeable power of a high voltage battery based on the determined state. The regenerative braking of the driving motor is then adjusted to prevent actual power of the regenerative braking of the driving motor from exceeding the allowance power of the regenerative braking.