Helium is a rare inert gas with indispensable applications in defense, aerospace, and medicine. However, helium resources available for use in China are extremely limited. To date, no independently accumulated helium resources have been found. Helium is primarily found in two forms: natural gas-associated and geothermal water-dissolved. This study focused on two typical basins—the Hangjinqi area in the northern Ordos Basin and the Weihe Basin—to investigate the genesis of helium. Helium isotope mass spectrometry analysis, rock radioactive element analysis and other methods were conducted to test the assgciated gas, core samples and potential helium source rock in the surrounding areas of the study area. The results show that helium in the Hangjinqi area in the northern Ordos Basin is typically crust-derived. While in Weihe Basin, high volume fractions of mantle-derived helium (up to 6.959%) were detected near deep-seated faults penetrating the basement, such as the Baoji-Xianyang fault and the Piedmont Fault of the Qinling Mountains. Both basins are located on the southwestern margin of the North China Plate and share a basement composed mainly of Archean-Proterozoic metamorphic-granite complexes, which serve as the main source rocks of helium formation. In addition, the main source rocks for helium gas in the Weihe Basin also include the uranium-rich granites of the Yanshanian period around the periphery and the concealed granitic bodies of the same period in the deep part of the basin. Due to the low mass fractions of U and Th elements or the low helium gas content of the desorbed gas in the basement sedimentary rock complexes, they cannot be regarded as the main source rocks for helium gas. The formation, migration and accumulation of helium gas in both areas are controlled by the source rocks and faults, and are closely related to the distribution of deep-seated fault zones. These findings provide a scientific basis for the further exploration and development of helium resources in the Weihe and northern Ordos basins.