A hydrogen compressor system comprises a hydrogen generating apparatus for generating hydrogen gas to be supplied to a fuel cell vehicle and a multi-stage reciprocating compressor for pressurizing the hydrogen gas generated by the hydrogen generating apparatus. High pressure tanks having maximum use pressure of 20 MPa are connected to middle stages of the multi-stage reciprocating compressor by gas supplying lines via valves. By opening/closing the valves, hydrogen gas in the high pressure tanks can be selectively supplied to the middle stages of the multi-stage reciprocating compressor.