A hydrogen supply system for a fuel cell and a control method thereof includes a fuel cell, a hydrogen supply line connected to an inlet side of an anode of the fuel cell and supplying hydrogen to the fuel cell, a hydrogen supply pressure sensor configured for measuring pressure of the hydrogen supply line, and a controller electrically connected to the hydrogen supply pressure sensor and configured for deriving a correction value of the hydrogen supply pressure sensor, supplying hydrogen after air supply is cut off during an operation of the fuel cell, measuring a pressure variation of the hydrogen supply line, and determinin g whether to use a correction value of the hydrogen supply pressure sensor based on the measured pressure variation.