Abstract: To improve the stability and comparability of handheld detection data in soil hydrogen geochemical exploration, field comparative experiments are conducted in the hydrogen seepage zone of the Zhangbei Basin. Using a comparative detection system for handheld electrochemical detector and gas chromatograph, we perform laboratory dynamic response experiments with a standard gas and in-situ sampling comparison experiments, and systematically analyze the dynamic response characteristics, stage-dependent bias patterns, and sampling timing optimization of the GA5000 handheld detector. Experimental results show that within the concentration range of 176–838 ppm, the detector requires more than 115 s to reach a stable state, and the stabilized reading deviates from the gas chromatography value by up to −68.8%; when the concentration increases to 1000 ppm, the stabilization time is shortened to approximately 100 s, and the deviation decreases markedly to nearly zero. Field sampling further reveals that the direction of hydrogen concentration change strongly affects the discrepancy between the two instruments: during the rising stage, gas chromatography values are generally higher than synchronous handheld readings, with a maximum deviation of 58.9%; during the declining stage, gas chromatography values are significantly lower than handheld readings, with a maximum deviation of 218.2%. Based on these findings, we propose a stage-specific differential sampling strategy and establish a calibration method of "synchronous comparison + local correction", forming a complete technical workflow that integrates rapid field screening, stage identification, sample collection, and gas chromatographic quantification. This work provides a technical reference for identifying surface gas seeps of natural hydrogen, correcting soil gas geochemical exploration data, and standardizing natural hydrogen surface detection procedures.