Accurate quantification of ultra-trace impurities in hydrogen, e.g., <0.004 μmol·mol−1 for total sulfur compounds as specified in ISO 14687-2019, is of paramount importance to ensure the quality of hydrogen for fuel cell vehicles. Here, we developed a novel fill-less trap pre-concentration inlet system integrated with GC-SCD for measuring ultra-trace sulfides in hydrogen. This analytical system can achieve an optimum method detection limit range of 0.002–0.004 nmol mol−1 (ppb(v)) for sulfides by trapping 400 mL hydrogen sample. The modified fill-less trap inlet system can avoid the deviation of desorption efficiency from adsorbents and shows a wide linearity range of up to 150 ppb(v) in 400 mL that is one order of magnitude higher than existing packing pre-concentration. Response sensitivity biases from the calibration pattern of constant volumes exhibit better sensitivity with deviation of up to ∼10% smaller than constant concentrations at 0.1–10.0 ppb(v). The stability of sulfides in hydrogen at 0.1–4.0 ppb(v) stored in Silonite™ canisters are firstly investigated. Poor stability is observed for H2S and EtSH of which each about 30% loss after 3 days storage, indicating that the hydrogen sample stored in Silonite™ containers should be analyzed within 4 days. Therefore, the developed analytical system with appropriate calibration pattern is well suitable for the accurate quantification of trace sulfides in hydrogen sampling from refueling station and production processing.