The invention discloses a fuel cell internal resistance adjusting method and system. The system includes a galvanic pile, an air supply device and a fuel cell controller. The air supply device comprises a compression unit, a cooling unit and a humidifying unit which are communicated in order. The humidifying unit is electrically connected to the fuel cell controller. The exhaust port of the humidifying unit is communicated with the air inlet of the galvanic pile. The compression unit includes a compressor and a first detecting component, and the first detecting component is configured to detect pressure and temperature of environment air at the intake end of the compressor. The cooling unit includes a cooler and a second detection component for detecting exhaust pressure and exhaust flow at the exhaust end of the cooler. Based on the adjusting method and an adjusting device, the internal resistance of a fuel cell can be accurately adjusted to allow the fuel cell to work in an optimum range, the efficiency of the entire galvanic pile is improved, and fuel cell damage caused by too low or too high relative humidity of the air in the galvanic pile can be effectively avoided, and service lifetime and the working efficiency of the galvanic pile are ensured.