Helium is a scarce strategic resource. Currently, all economically valuable helium resources are found in natural gas reservoirs. Owing to helium’s different formation and migration processes compared to natural gas’s, the traditional method of collecting wellhead gas to detect helium concentration may miss helium-rich layers in the vertical direction, which will not only cause the waste of helium resources, but also restrict the study of helium migration and accumulation mechanisms. To solve this problem, we designed a helium detector based on a quadrupole mass spectrometer. Through the combination of different inlet valves, we avoided gas mixing between different vertical layers during the inlet process and realized high-spatial-resolution helium concentration detection. We applied the helium detector to the Dongsheng gas field in the northern Ordos Basin, and the instrumental detection results were consistent with the laboratory analysis results of the wellhead gas, which demonstrated the stability of the helium detector in the field environment and the reliability of the data. Meanwhile, the results showed that the distribution of helium in the plane is highly heterogeneous, and the natural gas dessert layers and the helium dessert layers do not coincide in the vertical direction. In addition, we found a good correlation between helium and hydrogen concentrations. Combining our results with previous data, we propose a hydrogen–helium migration and accumulation model, which enriches the understanding of helium accumulation mechanisms and provides a basis for future helium resource exploration.