The invention relates to a gas filling system for a high-pressure hydrogen filling station, which comprises a control system, a sampling system, a filling system, an alarm system and a nitrogen purging system, and is the gas filling system which can collect hydrogen sample of the hydrogen filling station and fill high-pressure hydrogen for fuel cell powered vehicles. The gas filling system has the functions of temperature automatic compensation of filling measurement, selectable gas taking procedure in three-stage order, reasonable control of filling rate, alarm of hydrogen leakage and automatic power-down, pulling out prevention and automatic static release in the filling process, overpressure protection of the system, and so on. The sampling points are designed at the tail end of the whole flow of the hydrogen filling station, so that the acquired hydrogen sample can have more representativeness in quality; and through the design of pressure regulation treatment on the high-pressure hydrogen for sampling, the sampling operation is more simple, convenient and quick, and a regular gas sampling steel bottle can also be used together, thereby the sampling cost is low. The gas filling system can improve the gas taking rate of the hydrogen filling station and ensure that the temperature rise of a filled vehicle hydrogen storage tank is strictly controlled within the required temperature range in the quick hydrogen filling process.